[bionet.molbio.seqnet] SEQNET Bulletin

daemon@ig.UUCP (11/03/87)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 44  From:  Graham Cameron  29 October 1987  a job ad for your bulleti
From: Graham Cameron
 <CAMERON@EARN.EMBL> 29-OCT-1987 21:07
To: MJB1
Date: 29 October 1987
Subject: a job ad for your bulletin board


Via:            UK.AC.RL.EARN; Thu, 29 Oct 87 21:07:33 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 3787; Thu, 29
                Oct 87 21:07:33 GM
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                Thu, 29 Oct 87 21:07:32 GM
Date:           Thu, 29 Oct 87 21:14:17 n
To:             mjb1@UK.AC.CAM.VMS-SUPP
From:           Graham Cameron <CAMERON@EARN.EMBL>
Organisation:   European Molecular Biology Laboratory
Postal-address: Meyerhofstrasse 1, 6900 Heidelberg, W. Germany
Phone:          +49 (6221) 387-0 [switchboard]  +49 (6221) 387-257 [direct]
Subject:        a job ad for your bulletin board


                   Programming Posts in the EMBL Data Library


The EMBL Data  Library,  in  collaboration  with  the  American  GenBank  group,
produces  databases  of nucleotide and protein sequence data abstracted from the
research and patent literature and provided directly by researchers.   The  data
are  currently  being installed in an ORACLE based system running under VMS on a
VAX cluster  comprising a VAX 8600 and  a VAX 11/785.  The data are  distributed
throughout  the  world,  reaching  a user community of some 10000 researchers in
molecular biology.  Planned developments in the services  offered,  particularly
in  the  area of network access to the data, have created a need for Experienced
Applications Programmers, probably graduates, with a thorough  understanding  of
modern programming practice.

          Applications Programmer (Data Management)   Reference: 87/36

           o  to   work   on   the   development    of    ORACLE-based
              data-management  systems  and  the  transfer of existing
              data collections to these systems;

           o  develop data entry and update software for use  in-house
              and perhaps at other sites;

           o  explore the requirements for,  and  participate  in  the
              development of better data representation schemes;

           o  participate  in  the  development  of  online  retrieval
              systems  to  be  made  available  via  computer networks
              throughout Europe;

           o  help with the  development  of  systems  to  relate  our
              databases to other collections throughout the world.


          Applications Programmer (The User View)     Reference: 87/37

           o  to explore the needs of the world-wide user community;

           o  develop ways of making the data more  readily  available
              to  users  in  widely  differing computing environments,
              ranging from large mainframe to PC users;

           o  work with new distribution media (e.g., CD-ROM);

           o  participate  in  the  development  of  online  retrieval
              systems  to  be  made  available  via  computer networks
              throughout Europe;

           o  help  with  the  transfer  of  some  imported  PC  based
              software to our VAX cluster.

The EMBL Data Library is a  group  within  the  BioComputing  Programme  of  the
European  Molecular  Biology  Laboratory,  an  international  research institute
located in  Heidelberg,  West  Germany.   It  provides  a  stimulating  research
environment, and computing resources comprising a VAX cluster, SUN workstations,
a network of Macintosh personal computers, and various powerful graphics devices
including  an  Evans and Sutherland PS350 vector graphics display, all connected
by Ethernet.  Connections to EARN/BITNET and DATEX-P allow world-wide electronic
communication.

We  offer  an  above-average  salary  plus family, children's  and  non-resident
allowances,   depending  on  personal  circumstances.    Write  briefly  for  an
application form, quoting the appropriate reference, to:

EMBL Personnel Section
Postfach
D-6900 Heidelberg
West Germany.

daemon@ig.UUCP (11/10/87)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 45  From:  MJB1  7 November 1987  Please mail you sequences to DATASU
From: MJB1
Date: 7 November 1987
Subject: Please mail you sequences to DATASUBS%EMBL@UK.AC.RL.EARN

                EMBL/GenBank SEQUENCE DATA SUBMISSION FORM



This form solicits the information needed for a nucleotide and/or amino acid
sequence data bank entry.  It can be filled in using any text editor or printed
and filled in by hand.  By completing and returning it to us promptly you will
help us enter your data in the appropriate database accurately and rapidly.
Where appropriate, the data will be transmitted to the SWISS-PROT and the PIR
protein sequence databases.

Please answer all questions which apply to your data.  If you are reporting two
or more non-contiguous sequences, please copy and fill out this form for each
additional sequence.  Then send us (1) this form, (2) the sequence data, and
(3) a pre- or reprint of your manuscript.  You can send these materials (a)
electronically via computer network, (b) on magnetic tape, or (c) on a floppy
diskette.  Please do NOT send the sequence as a computer printout, as this
creates considerable extra work for us.  Information about formats for
submitted data is included at the end of this form.

   our mailing address:    EMBL Data Library Submissions
                           Postfach 10.2209
                           D-6900 Heidelberg
                           West Germany

   telephone:              (06221) 387 257

   network address:        datasubs@embl.earn  (for data submissions)
                            datalib@embl.earn  (for general inquiries)

Please include in your submission any additional sequence data which may not
reported in your manuscript but which has been reliably determined (for
example, introns or flanking sequences).

When we receive your sequence data and the completed form we will assign the
sequence an accession number, which serves as a reference that permanently
identifies this sequence (or set of sequences) in the database.  We will inform
you what number your data has been given and we recommend that you cite this
number when referring to the corresponding sequence in a publication.  A large
number of journals are actively supporting the practice of citing sequences by
accession number.

If new data become available which would make the database entry more
informative (e.g., function of the gene product or location of important sites
within the sequence), or if you discover errors in the sequence, we urge you to
contact us so that we can update your entry.


===============================================================================
  Your name
 ------------------------------------------------------------------------------
  Organization
 ------------------------------------------------------------------------------
  Address



 ------------------------------------------------------------------------------
  Telephone                     Computer network address
 ==============================================================================
  On what medium and in what format are you sending your sequence data? (see
  end of this form for instructions)
      [ ] magnetic tape: density   [ ] 800  [ ] 1600   [ ] 6250
                         character code  [ ] ASCII  [ ] EBCDIC
                         record length ______________ blocksize ______________
                         label type _________________
      [ ] electronic mail
      [ ] diskette: computer ________________ operating system _______________
      [ ] printed copy
===============================================================================


CITATION INFORMATION

===============================================================================
  These data will be published by
  authors
 ______________________________________________________________________________
  title of paper
 ______________________________________________________________________________
  journal
 ------------------------------------------------------------------------------
  vol, pages,year (if known)
 ==============================================================================
  Does the sequence which you are sending with this form include data that
  does not appear in the above journal article?
     [ ] yes, beginning at base number _____ and ending at base _____   [ ] no
  How should this data be cited in the database?
     authors
 ------------------------------------------------------------------------------
     title of paper (if applicable)
 ------------------------------------------------------------------------------
     journal (if applicable)                       vol,pages,year
 ==============================================================================
  Please list references to papers and/or database entries which report
  sequences overlapping with data submitted here.
 ------------------------------------------------------------------------------
     first author     journal, vol., pages, year OR database, accession number
 ------------------------------------------------------------------------------

 ------------------------------------------------------------------------------

 ==============================================================================


DESCRIPTION OF SEQUENCED SEGMENT

Where appropriate, please use standard nomenclature or conventions. NOT ALL
QUESTIONS ARE RELEVANT TO ALL SEQUENCES.
===============================================================================
 What kind of molecule does this sequence represent?

  [ ] genomic DNA                                      [ ] tRNA
  [ ] organelle DNA (please specify) ______________    [ ] rRNA
  [ ] cDNA                                             [ ] snRNA
  [ ] other nucleic acid __________________________    [ ] scRNA

  [ ] peptide
      sequence assembled by  [ ] overlap of sequenced fragments
                             [ ] homology with related protein sequence
                             [ ] other (please specify) _____________________
-------------------------------------------------------------------------------
 length of sequence          [ ] bp   or   [ ] amino acid residues
-------------------------------------------------------------------------------
 library (type, name)                      clone(s)
-------------------------------------------------------------------------------
 genomic location/map position             gene name(s) (e.g., lacZ)
-------------------------------------------------------------------------------
 gene product name(s) (e.g., beta-D-galactosidase) and Enyme Commission number

-------------------------------------------------------------------------------
 source organism (Latin name) (e.g., Mus musculus)
-------------------------------------------------------------------------------
 strain (e.g., BALB/c)                     haplotype
-------------------------------------------------------------------------------
 tissue/cell line source                   [ ] germ line     [ ] rearranged
===============================================================================


FEATURES OF THE SEQUENCE

Please list below the first and last base/residue numbers of all significant
features identified within the sequence.  In the column marked "id," indicate
the method by which the feature was identified (E = experimentally; S = by
similarity with another sequence; C = match to an established consensus
sequence).  For nucleotide sequences, indicate (by writing an x in the column
marked "comp") if the feature is encoded by the strand complementary to that
reported here.

Some examples of significant features are:

  - regulatory signals (e.g., promoters, attenuators, enhancers)
  - transcribed regions (mRNA, rRNA, tRNA, etc.)
  - regions subject to post-transcriptional modification (e.g., introns,
    modified bases)
  - translated regions
  - extent of signal peptide, prepropeptide, propeptide, mature peptide
  - sites subject to post-translational modification (glycosylation,
    phosporylation)
  - other domains/sites of interest (e.g., extracellular domain, DNA-binding
    domain, active site, inhibitory site)
  - sites involved in bonding (disulfide, thiolester, intrachain, interchain)
  - regions of alpha helix or beta pleated sheet

================================================================================
   Numbering for features on the sequence you are submitting to us
       [ ] starts at 1   OR    [ ] starts at _______
   Does the numbering match that in your manuscript?   [ ] yes   [ ] no
--------------------------------------------------------------------------------
                   feature                    from       to       id     comp
------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

================================================================================



KEYWORDS

===============================================================================
Describe the properties of the sequence in terms of its associated
phenotype(s), the biological/enzymatic activity of its product and the general
functional classification of the gene and/or gene product.  Also indicate
macromolecules which the gene product can bind (e.g., DNA; Ca++; other
proteins), subcellular localization of the gene product and any other
information you think is relevant.

EXAMPLE (for the viral erbB gene sequence): transforming capacity;
EGF receptor-related; transmembrane protein; tyrosine kinase; oncogene.
-------------------------------------------------------------------------------



===============================================================================




FORMATS FOR SUBMITTED DATA

We can accept data submitted in any of the following formats, listed in order
of preference.  PLEASE SEND THE SEQUENCE DATA IN COMPUTER-READABLE FORM rather
than as a printout.

(1) Electronic file transfer: files can be sent via computer network to
    DATASUBS@EMBL.EARN.  This address can be reached via various gateways from
    Arpanet, Usenet, JANET, JUNET, etc.  Ask your local network expert how to
    send to BITNET/EARN or phone us for help at (06221) 387 257.

(2) Magnetic tapes: 9-track only (fixed-length records preferred); 800, 1600 or
    6250 bpi (any blocksize); ASCII or EBCDIC character codes; any label type
    or unlabelled.

(3) Floppy disks: we can read 5-1/4" diskettes from CP/M or MS-DOS
    systems, as well as Macintosh diskettes.  Phone us if you have questions
    about your specific format.


Whatever format you choose, we would appreciate receiving the sequence data in
a form which conforms to the following conventions:

    Each distinct sequence should be listed separately using the same number
    of bases/residues per line and its length in bases/residues clearly
    indicated.

    Nucleotide sequences should be shown in the 5' to 3' direction.  If both
    strands are listed, the top strand should be 5' to 3'.

    Enumeration of nucleic acid sequences should begin with a "1" and ascend
    in the direction 5' to 3'.

    Amino acid sequences should be listed using the one-letter code.

The code for representing the sequence characters should conform to the
IUPAC-IUB standards, which are described in the following references.

    for nucleic acids:  Eur. J. Biochem. 150, 1-5, 1985

    for amino acids:    J. Biol. Chem. 243, 3557-3559, 1968
                        Eur. J. Biochem. 5, 151-153, 1968

daemon@ig.UUCP (11/25/87)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 49  From:  MA11  24 Nov 87  Drosophila codon table 3.0
Date: 24 Nov 87
From: MA11
Subject: Codon tables
To: seqnet

                   Drosophila Codon Table

                      Version 3.0

                   Michael Ashburner,
                 Department of Genetics,
                 University of Cambridge,
                    Cambridge, England.

              Telephone 44-(0)223-333969
              Electronic mail:ma11@uk.ac.cam.phx

                      November 20 1987

These Tables are supplied with the understanding that they can be freely used
for research, although if quoted in any publication a suitable acknowledgement
(e.g. Michael Ashburner, personal communication) would be appreciated.

I will automatically post new versions on the SEQNET and BIONET Bulletin
Boards. These will generally be compiled whenever enough new data warrents
the work. I am very happy to include new sequences that have not yet made
the Sequence Data Banks, if these can be sent to me by electronic mail
with sufficient data for the coding sequences to be extracted. If anyone
should need the files of coding sequences that have been used to generate
these tables please send me a message.


Two series of Table are included, one for "host" genes and one for orfs carried
by transposable elements. For each series you have a codon table, a base
composition and the names of the sequences used to compile these.

By and large these sequences are taken from the EMBL, GENBANK or DAYHOFF
Libraries. However some have been privately communicated to me. All sequences
have been checked that they translate but many are incomplete. Hence, for
example, the number of sequences is greater than the number of TER codons.

The latest versions of the databanks used are EMBL V13.0 and GENBANK V52.0.
//
Table 1A: Codons of "host" genes:
     TTT       401     TCT       256     TAT       416     TGT       254
     TTC      1075     TCC       902     TAC      1006     TGC       743
     TTA        91     TCA       218     TAA        50     TGA        15
     TTG       572     TCG       689     TAG        22     TGG       486

     CTT       264     CCT       288     CAT       413     CGT       448
     CTC       523     CCC      1002     CAC       735     CGC       814
     CTA       253     CCA       491     CAA       458     CGA       268
     CTG      1734     CCG       669     CAG      1554     CGG       294

     ATT       631     ACT       344     AAT       732     AGT       325
     ATC      1237     ACC      1222     AAC      1222     AGC       777
     ATA       225     ACA       313     AAA       491     AGA       169
     ATG      1084     ACG       568     AAG      1998     AGG       226

     GTT       476     GCT       686     GAT      1198     GGT       798
     GTC       773     GCC      1870     GAC      1153     GGC      1495
     GTA       179     GCA       408     GAA       602     GGA       988
     GTG      1307     GCG       533     GAG      2139     GGG       175

Total=43748
//
Table 1B: Base composition of "host" genes:
T=25951 C=37217 A=30973 G=37107  Nucleotides=131256
//
Table 1C: "Host" gene sequences used for Tables 1A and 1B

                      [EMBL/GENBANK Acession numbers]
M14643;                      alpha-tubulin-1
M14644;                      alpha-tubulin-2
M14645;                      alpha-tubulin-3
M14646;                      alpha-tubulin-4
K00667-K00669;               Actin 5C
K00670;K00671;               Actin 42A
J01064;                      Actin 79B
K00674;K00675;               Actin 87E
J01065;                      Actin 88F
Z00030;                      Alcohol dehydrogenase and 3' ORF
X04695;                      amd
X04569-X04570;               amylase-2
X03788-X03791;               Antp
M14549;                      bicoid
X04896;                      bsg25D
M14131;                      C1A9 nuclear protein
K01042;                      c-ash
M11281;                      c-myb (13E)
K01960;                      c-ras1 (85D)
M10759;M10803;M10804;        c-ras2 (64B)
X02200;                      c-ras3 (62B)
M11917;                      c-src (64B)
X02305;                      c-src4
Y00133;                      calmodulin
X03062;                      caudal
M13219;                      choline acetyl transferase
X02497;                      chorion genes s18-1, s15-1 and s19-1
V00200;                      collagen-like gene fragments [two genes]
X01761;                      cytochrome c gene DC3
X01760;                      cytochrome c gene DC4
M13373;                      Deformed
X04426;                      dopa decarboxylase
M14978-14982;                dunce
X04521;                      eip28/29
Cherbas;                     eip40
M11744;                      Elongation factor (48D)
M10017;                      engrailed
K03416;K03417;K034018;       epidermal growth factor homolog
Richmond;                    Esterase-6
X05138;                      eve
X00854;K01951;               ftz
M11254;                      Gapdh-1
M11255;                      Gapdh-2
J02527;                      glycinimide ribotide transformylase (GART)
M13786;                      Gpdh [exon 3]
J01085;                      heat shock cognate 70C [exon 1]
K01296;K01297;               heat shock cognate 87D [exons 1 & 2]
J02569;                      heat shock cognate 88E
X04073;                      Histone H1
Dayhoff;                     Histone H2A
Dayhoff;                     Histone H2B
Dayhoff;                     Histone H3
Dayhoff;                     Histone H4
V00209;                      hsp22
V00210;                      hsp23
V00211;                      hsp26
V00212;                      hsp27
V00213;V00214;               hsp70 [87A]
J01104;J01105;               hsp70 [87C]
X03810;                      hsp82
Y00274;                      hunchback
M13568;                      Insulin-like receptor protein-1
M14778;                      Insulin-like receptor protein-2
K03057;K03058;               invected
X04227;                      l(2)37Cc
V00202;                      larval cuticle protein I [44D]
V00203;                      larval cuticle proteins II & III [44D]
V00204;                      larval cuticle proteins H, D and L.
X03872;                      LSP1-alpha
X03873;                      LSP1-beta
X03874;                      LSP1-gamma
X03758;                      metallothionein  (Mtn)
M12741;                      myosin-heavy chain [exons A & C]
M10125;                      myosin-light chain
X04016;                      nicotinic acetylcholine receptor (AChR)
K02315;                      ninaE (opsin)
M11664;                      Notch
Y00043;                      ospsin R7 specific
M12896;                      opsin at 91D
M15762;                      pen#9b
M11969;                      period
Y00402;                      Phosphoenolpyruvate carboxykinase
M14548;                      prd
X05076;Y00042;               protein kinase C
X00848;                      ribosomal protein rp49
X05016;                      ribosomal protein rp1A
M11798;                      RNA polymerase II-215
Y00308;                      rosy
X04813;                      rudimentary
X01918;                      Sgs3, Sgs7, Sgs8
J01135;J01136;               Sgs4
X04269;                      Sgs5
X04513;                      snake
X03121;                      sry
K03277;                      tropomyosin I
M15466;                      tropomyosin II
X02989;                      trypsin-like enzyme, alpha-chain
X05723;Y00206;               Ubx
X01802;                      vitelline membrane protein
X02974;                      white
Chia;                        yellow
V00248;                      Yolk protein-1
J01157;                      Yolk protein-2
M15898;                      Yolk protein-3
//
Table 2A: Codon table TE genes:
     TTT       366     TCT       129     TAT       264     TGT       108
     TTC       200     TCC       120     TAC       230     TGC       107
     TTA       351     TCA       197     TAA         1     TGA         1
     TTG       195     TCG        74     TAG         0     TGG       108

     CTT       216     CCT       112     CAT       187     CGT        64
     CTC       104     CCC       104     CAC       165     CGC        38
     CTA       199     CCA       271     CAA       396     CGA        99
     CTG       105     CCG        52     CAG       160     CGG        22

     ATT       463     ACT       205     AAT       620     AGT       180
     ATC       175     ACC       171     AAC       403     AGC       145
     ATA       447     ACA       374     AAA       888     AGA       260
     ATG       199     ACG        64     AAG       282     AGG        83

     GTT       181     GCT       160     GAT       330     GGT       130
     GTC       106     GCC       129     GAC       305     GGC       107
     GTA       188     GCA       222     GAA       566     GGA       148
     GTG       113     GCG        63     GAG       227     GGG        39

Total=12718
//
Table 2B: Base composition TE genes:
T=9774 C=7350 A=14591 G=6439  Nucleotides=38154
//
Table 2C: TE genes used for Tables 2A and 2B:

                  [EMBL/GENBANK Accession numbers]
X01472;                      17.6 element
X03431;                      297 element
X04132;X03733;               412 element
X02599;                      copia element [Saigo]
V00246;                      FB4
X03734;                      gypsy element
X01748;                      HB1
X04705;                      hobo
Finnegan                     I element
O'Hare;                      P element
X01747;                      transposon HB2
X02600;                      virus like particle RNA (VLP H-RNA)
//

MJB1@VMS-SUPP.CAM.AC.UK (12/10/87)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 49  From:  MJB1  10 December 1987  HMMI Human Gene Mapping Library
From: MJB1
Subject: HMMI Human Gene Mapping Library
Date: 10 December 1987

                      HUMAN GENE MAPPING LIBRARY
The Human Gene mapping Library at New Haven (HGML), funded by the Howard
Hughes Medical Institute, consists of five interconnected databases.
These databases are of particular interest to those working in human
genetics; they are currently maintained on an IBM 4341 mainframe computer
at Yale University.  The databases are:
 LIT      literature citations and abstracted information
 MAP      mapped genes information
 PROBE    information on probes
 RFLP     restriction fragment length polymorphism data
 CONTACT  names and addresses of researchers to contact
          for probes

Online database access is possible from the UK but the IPSS telephone
charges have to be paid for by the user.  Charges for computer usage
are at present absorbed by the Howard Hughes Medical Institute.
To access the computer from a terminal connected to a PAD on Janet,
first call the IPSS Gateway:

CALL LON.PSS
or
CALL 00004000004096

Then, using your PSS account identifier and password call the Yale
computer on Telenet:

(XX10,SECRET).NFS-31102030002100/GENES

At the ENTER CLASS prompt type VMF and press RETURN a few times.
When asked ENTER TERMINAL TYPE respond with HCPY
The computer now ask for a LOGON userid.
You should obtain details of logging on and your own personal
password from:
Deborah A. Consiglio
Human Gene Mapping Library
25 Science Park Suit 457
New Haven
CT 06511
USA                      Tel. 203 786 5519

It is also possible to request information by electronic mail
at the address GENELIB%YALEVM@UK.AC.RL.EARN
Please be sure to include your return address (electronic or postal).

MJB1@VMS-SUPP.CAM.AC.UK (12/11/87)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 50  From:  MJB1  11 December 1987  Index to SEQNET Bulletins
From: MJB1
Date: 11 December 1987
Subject: Index to SEQNET Bulletins

SEQNET has now been operating for just over a year.  Many thanks to all
our contributors.  Keep the messages coming in 1988.
Note: the numbering here is the official version. A slight hitch in numbering
occurred around  47 in the bulletins distributed.

Bulletin 49  From:  MJB1  10 December 1987  HMMI Human Gene Mapping Library
Bulletin 48  Graham Cameron  25 Nov 1987 Posts in the EMBL Data Library
Bulletin 47  From:  MA11  24 Nov 87  Drosophila codon table 3.0
Bulletin 46  From:  DPJ10  13 Nov 1987  Computing course
Bulletin 45  From:  MJB1  7 November 1987  Please mail you sequences to DATASUBS
Bulletin 44  From:  Graham Cameron  29 October 1987  a job ad for your bulletin
Bulletin 43  From:  RS12  27 October 1987  EARN/ARPA connection
Bulletin 42  From:  David Judge  22 October 1987  STADEN Plus
Bulletin 41  From:  M.J.Bishop  21 October 1987  MSDN in Cambridge
Bulletin 40  From:  M.J.Bishop  20 October 1987  MINE
Bulletin 39  From:  MJB1%CAM.PHX@UK.AC.RL.EARN  29 September 1987  IUSC Workshop
Bulletin 38  From:  MJB1@CAM.PHX  15 Sep 1987  Miscellaneous
Bulletin 37  From:  TEETER@EARN.BCCHEM  9 Sep 1987  Addresses of crystallog. via
Bulletin 36  From:     BIOTECH@EARN.UMDC  20-AUG-1987 16:18  BIOTECH Bulletin Board
Bulletin 35  From:  MJB1@CAM.VMS-SUPP  20 Aug 1987  BIOTECH Bulletin Board
Bulletin 34   From:   SEQNET  Thu 16 Jul 87 18.2 Bionet Access (revised)
Bulletin 33   Drosphila Codon Tables
Bulletin 32  From:  MJB1  7 July 1987  NRC Industrial Biotechnology Conference
Bulletin 31  From:  MJB1  6 July 1987  Microorganisms and Patents
Bulletin 30  From:  MJB1  3 July 1987  Position at Louisiana State
Bulletin 29        PHYLIP Package       Joe Felsenstein
Bulletin 28   Drosophila codons
Bulletin 27  From:  DPJ10@CAM.PHX  16 June 1987  Staden programs on IBM PC
Bulletin 26  From:  DPJ10@CAM.PHX  12 June 1987  Computing Course
Bulletin 25  From:  MJB1@CAM.VMS-SUPP  12 June 1987  Molecular Biology Software
Bulletin 24  From:        SGM Computer Club <XBCF06%uk.ac.cardiff.geca@uk.ac>
Bulletin 23  From:         RS       5-JUN-1987 15:22  Staden Package
Bulletin 22  CODATA workshop: a reply from Joseph L. Modelevsky
Bulletin 21  REPLY TO CODATA MEETING REVIEW ON SEQNET
Bulletin 20   From:   MJB1  Thu 28 May 87 11.51 Course on DNA sequencing computi
Bulletin 19   From:   MJB1  Thu 21 May 87 16.19 Molecular biology computing work
Bulletin 18   CoData Meeting Summary
Bulletin 17   From:   SEQNET  Tue 12 May 87  9.2BIONET Bulletin Board3
Bulletin 16   From:   MJB1  Thu  7 May 87 17.16 MiCIS Microbial Culture Informat
Bulletin 15  From:  SXR::BEACHAM      27-APR-1987 12:19   27-APR-1987 19:52:48
Bulletin 14  From:  P.Taylor@uk.ac.glasgow.centre  Thu,16 Apr 87 10:18:52 BST  A
Bulletin 13  From:  Kristofferson    Tue 3 Mar 87 15:55:50-PST  Job vacancy.
Bulletin 12   From:   MJB1  Tue  3 Feb 87 18.16 Course on molecular biology comp
Bulletin 11  From: STOEHR@UK.AC.AFRC.ARCC         26-JAN-1902  Gel entry programs for
Bulletin 10   From:   MJB1  Sat 24 Jan 87 16.57 Public domain software for IBM P
Bulletin 9  From:   SYSTEM@UK.AC.BRISTOL.BSA   20-JAN-1987 12:09:58  Heliwheel p
Bulletin 8  From:   ABJA1248@UK.AC.QUB.V1   17-DEC-1986 09:02:58  Custom synthes
Bulletin 7  From:   Nigel Brown <BrownNL@UK.AC.AUCC>   Tue, 23 Dec 86 17:09 GMT
Bulletin 6  From:      ICRF Computing Units <rwy@uk.ac.ucl.cs>      Wed, 3 Dec 8
Bulletin 5  From: A.F.W.Coulson@uk.ac.edinburgh 02Dec86 Searching the protein se
Bulletin 4   From:   MA11  Wed 26 Nov 86 12.44 Sending data to EMBL
Bulletin 3   From:   MA11  Wed 26 Nov 86 12.39 Drosophila codon tables
Bulletin 2   From:   MJB1  Mon 24 Nov 86 21.56 SEQNET Bulletin Board

MJB1@VMS-SUPP.CAM.AC.UK (01/13/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 54  G.WILLIAMS@UK.AC.CRC  Tue 12 Jan 88 CHROMOSOME LOCATION DATABASE
From: G.WILLIAMS@UK.AC.CRC
authorisingUsers: POST@UK.AC.CRC
To: SEQNET@UK.AC.CAM.PHX
Subject: CHROMOSOME LOCATION DATABASE

Reply-to: G.WILLIAMS@UK.AC.CRC

Date: Tue 12 Jan 88 14:52:10-GMT
From: "Gary Williams, Computing Services, CRC" <G-WILLIAMS@CRC>
Subject: CHROMOSOME LOCATION DATABASE
To: seqnet%cam.phx@JANET
cc: g-wILLIAMS@CRC
Message-ID: <12366019183.15.G-WILLIAMS@CRC>


 Can anyone tell us where information/databases exist of chromosomal
locations of genes and anonymous DNA polymorphisms.

  Thanks, Gary Williams.
-------
==============

MJB1@VMS-SUPP.CAM.AC.UK (01/14/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 55  <HARPER@EARN.FINFUN> Wed, 13 Jan 88 AIDSNEWS... new newsletter
From: <HARPER@EARN.FINFUN> 13-JAN-1988 15:29
To: MJB1
Subj: AIDSNEWS... new newsletter


Via:           UK.AC.RL.EARN; Wed, 13 Jan 88 15:23:54 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 8198; Wed, 13
               Jan 88 15:23:54 GM
Received:      from FINFUN.BITNET (HARPER) by UKACRL.BITNET (Mailer X1.25) with
               BSMTP id 8197; Wed, 13 Jan 88 15:23:52 G
Date:          Wed, 13 Jan 88 17:25 O
From:          <HARPER@EARN.FINFUN>
Subject:       AIDSNEWS... new newsletter
To:            mjb1@UK.AC.CAM.VMS-SUPP
X-Original-To: mjb1@vms-supp.cam.ac.uk, HARPER

Dear Martin,

Some time ago I told you about a AIDS newsletter... nothing
ever seemed to come of it. However I have now discovered a new
newsletter called AIDSNEWS. It is sent out from Reutgers
University by Michael Smith. If you mail him at the address
below he can send you back issues... there are about 46 issues
at present. It is "alternative" treatments so some of the text
might not appeal to "conventional" scientists. Never the less
it covers much the same ground as the New Scientist's AIDS
MONITOR... at least I have put it up for reading for interested
scientists on our mainframe... Check it out.
%%%%%%%%%%%%%%%%%%%%%%%%%%EXTRACT%%%%%%%%%%%%%%%%%%%%%%%
From: Michael Smith <MNSMITH@UMAECS>
Date: Tue, 22 Dec 87 21:06:00 EST

        Today I added all of the subscribers of the Arpanet Aidsnews
list to Litserv AIDSNEWS. List AIDSNEWS now has over 200 individual
subscribers and is sent to internal distribution lists at many large
corporations and universities.
        Subscribers outside of Bitnet should send mail to:

AIDSNEWS%RUTVM1.BITNET@CUNYVM.CUNY.EDU

        Bitnet users, sorry you had to get this. Happy Holiday(s)!

                -- Michael
----------------------------------------------------------------
Michael Smith                     Bitnet: MNSMITH@UMAECS
155 Main Street                    CSnet: MNSMITH@ECS.UMASS.EDU
Northampton, MA 01060               Arpa: MSMITH@CS-UMASS.ARPA
%%%%%%%%%%%%%%%%%%%%%%%%END of EXTRACT%%%%%%%%%%%%%%%%%%%%%%%%

cb@LANL.GOV (01/14/88)

From: cb@lanl.gov (Christian Burks)

for G.Williams@uk.ac.crc

re: locations of genes and anonymous DNA polymorphisms

check with the Human Gene Mapping Library in New Haven for human
gene mapping info.

check "Genetic Maps" edited by Stephen O'brien for other organisms.

there is also something becoming a database collaboratively between
Ray White's group in Utah and a partner in Paris, focusing on
genetic polymorphisms in humans.

Christian Burks

MJB1@VMS-SUPP.CAM.AC.UK (01/15/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 58 SEQNET@CAM.PHX 14 Jan 88  List of European molecular biologists
From: SEQNET@UK.AC.CAM.PHX
Subject: List of European molecular biologists
Date: 14 Jan 88
A start has been made on compiling a list of electronic mail addresses
for European molecular biologists as suggested at the IUSC Workshop.
Please contribute an entry if you have not already done so.

*name Alefounder,P.R.
From: PRA1
To: seqnet
Subject: Address List for Europe

(1) Electronic mail address: JANET       PRA1@CAM.PHX
                             EARN        PRA1%CAM.PHX@EARN.RL.AC.UK

(2) Name and postal address: Dr. P.R. Alefounder,
                             Department of Organic & Inorganic Chemistry,
                             University Chemical Laboratory,
                             Lensfield Road,
                             Cambridge CB2 1EW.

(3) Indication of interests: Molecular biology, computers.


*name Beynon,R.B.
From: <SB06@UK.AC.LIVERPOOL.IBM> 11-JAN-1988 18:27
To: MJB1
Subj: Re: SEQNET Bulletin


Received:     from SB06@UK.AC.LIVERPOOL.IBM
              by ISMAIL(2.1.6);  11 Jan 1988 18:27:01 GMT
Date:         Mon, 11 Jan 88 18:24:00 GMT
From:         <SB06@UK.AC.LIVERPOOL.IBM>
Subject:      Re: SEQNET Bulletin
To:           MJB1 <MJB1@CAM.VMS-SUPP>
In-Reply-To:  Your message of 8-JAN-1988 18:27:29 GMT

Martin please add my info to the europe list:

SB06@UK.AC.LIV.IBM

Dr R J Beynon
Department of Biochemistry
University of Liverpool
PO Box 147
LIVERPOOL
L69 3BX
U.K.

Editor Computer Applications in the Biosciences
Mammalian proteases and cellular proteolytic processes
Protein metabolism in normal and abnormal muscle
Glycogen phosphorylase
Thaumatin ( a very, very sweet protein!!)
Apple Macintosh

*name Bishop,M.J.
From: MJB1
To: seqnet
Subject: European list

(1) MJB1@UK.AC.CAM.PHX
    MJB1@UK.AC.CAM.VMS-SUPP
(2) Martin John Bishop
   University of Cambridge,
   Computer Laboratory,
   New Museums Site,
   Pembroke Street,
   Cambridge CB2 3QG,
   UK.
(3) DNA and protein sequence analysis,
    Inference of evolutionary relationships from sequence data,
    Applications of computers in molecular biology

*name Evans,R.G.
From: "RGE" (RGE at UKACRL) <RGE@UK.AC.RL.IB> 12-JAN-1988 09:07
To: MJB1
Subj: Molecular Biology

Dear Dr Bishop,  I am interested in keeping in touch with the development
of molecular biology computing, although I am not active in this area.  My
interest stems from running the scientific side of Cray X-MP support at RAL
and I would like to help in the use of supercomputers wherever appropriate.
The information requested in your note is:
(1)  RGE@UK.AC.RL.IB
(2)  Dr R G Evans, Rutherford Appleton Laboratory
                   Chilton, Didcot  OX11 0QX  tel 0235 21900ext5656
(3)  Interested in new and developing areas of supercomputer applications.

*name Farrall,M.
From: rkbc110@uk.ac.lon.smhms.ux
To: seqnet@cam.phx

Martin Farrall
Department of Biochemistry and Molecular Genetics
St. Mary's Hospital Medical School
Norfolk Place
London  W2 1PG
(01) 723 1252

rkbc110@uk.ac.lon.smhms.ux

Molecular genetics of cystic fibrosis
DNA/protein sequence analysis
Computational methods in human genetic linkage analysis

*name Holbrook,J.J.
Date:  10-JAN-1988 14:41:34
From:  HOLBROOK@UK.AC.BRISTOL.BSA
To:  mjb1@UK.AC.CAM.VMS-SUPP

SEQNET - Address list for Europe

1. JANET:        HOLBROOK@UK.AC.BRISTOL.BSA

2. Dr J. John HOLBROOK,
   Department of Biochemistry,
   University of Bristol Medical School,
   BRISTOL BS8 1TD,
   U.K.

3. Protein, especially redox enzyme, design and construction.

4. It would help if the one of my long term collabroators
   were also included, with an otherwise analogous entry:
   Dr. A.R. CLARKE:    CLARKEAR@UK.AC.BRISTOL.BSA


*name Kell,D.B.
From: DBK@UK.AC.ABERYSTWYTH
To: SEQNET@UK.AC.CAM.PHX
Subject: e-mail adresses

In response to today's, I presently act as the main node at UCW for
biological bboard services, and this will continue pro tem. When my
colleague sget more into it they will doubtless join directly.
However, please keep me on the list for SEQNET info.
(1) DBK@ABER.V
(2) Dr Douglas B. Kell, Dept of BOtany & Microbiology, University
College of Wales, ABERYSTWYTH, Dyfed SY23 3DA.
(3) Interests: keeping abreast with everything relevant in mol.
biol., but especially protein behaviour and use of micro's to
understand it.
Best wishes for 1988!

*name Kneale,G.G.
From: GGK1
To: seqnet@cam.phx
Subject: MOLECULAR BIOLOGY NETWORK

Please include me in your list of molecular biology network users:
    Dr Geoff Kneale
      Biophysics Laboratories
       Portsmouth Polytechnic
        Portsmouth  PO1 2DT

      GGK1@PORTSMOUTH.CSOVAX

AREAS OF INTEREST:  DNA binding proteins, Protein Engineering, Filamentous
                    Bacteriophage, Biophysics (Spectroscopy and Diffraction).

*name Melvin,W.T.
From: w.t.melvin@uk.ac.aberdeen
To: seqnet@uk.ac.cambridge.phoenix
Subject: Address List for Europe

With reference to your message of 8 Jan;
Electronic mail address           W.T.MELVIN@UK.AC.ABDN
Postal address                  Dr W.T. Melvin
                                Dept. of Biochemistry
                                University of Aberdeen
                                Marischal College
                                Aberdeen, AB9 1AS
                                U.K.
Tel No.                 0224 273110

Interests               Molecular biology of cytochrome P450
                        and DNA polymerase alpha

*name Pfeiffer,F.
From: PFEIFFER@EARN.DM0MPB51
To: SEQNET@UK.AC.CAMBRIDGE.PHOENIX
Subject: electronic mailing address list

Via:           UK.AC.RL.EARN; Mon, 11 Jan 88 14:39:19 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 2094; Mon, 11
               Jan 88 14:39:18 GM
Received:
           from DM0MPB51.BITNET (PFEIFFER) by UKACRL.BITNET (Mailer X1.25) with
               BSMTP id 2084; Mon, 11 Jan 88 14:38:40
X-Original-To: g--seqnet, PFEIFFER

                                   11-JAN-1988
Dear Dr. M.J. Bishop!
The members of the MIPS protein sequence database would like to participate in
the European electronic mailing address list:
MIPS postal address is:
MIPS (Martinsried Institute for Protein Sequence Data)
Max-Planck-Institute for Biochemistry
Am Klopferspitz 18
D-8033 Martinsried
FRG
Current members are:
Dr. Friedhelm Pfeiffer
Dr. Hans Werner Mewes
Electronic Mailing addresses are:
MIPS@dm0mbp51.BitNet     sequence submission and general information
Pfeiffer@dm0mpb51.BitNet personal messages, VecBase, restriction enzymes
Mewes@dm0mpb51.BitNet    personal messages
MIPS interest:
MIPS is a protein sequence database that will collect and distribute protein
sequences within the frame of a protein sequence database consortium. The
three current members are
   MIPS  at Max-Planck-Inst. Biochemie,   Martinsried, FRG,   in Europe
   PIR   at MBRF (Nat. Biomed. Res. F.),  Washington,  USA,   in America
   JIPID at Science University,           Tokyo,       Japan, in Asia
The members of this consortium will prepare one common sequence data set. This
will be an extension of the current PIR protein sequence database. Data
submission and comments via electronic mailing are highly recommended.
Please send SeqNet mail to user "MIPS" in the future and discontinue sending
to "PFEIFFER" and "MEWES".
Yours sincerely
                 Friedhelm Pfeiffer

*name Stoehr,P.J.
From: STOEHR@UK.AC.AFRC.ARCC
To: SEQNET@UK.AC.CAM.PHX

I would like to participate in the great European database in the sky.

(1) STOEHR @UK.AC.AFRC.ARCC
(2) Peter J. Stoehr
    Applications Development
    AFRC Computing Centre
    West Common
    Harpenden
    Hertfordshire AL5 2JE
    Tel. 05827-62271
(3) Computing Service/Support for Molecular Biology

also
 (1) OWEN @UK.AC.AFRC.ARCB     (note B)
 (2) Dr John Owen
     (same address)
 (3) Computing Service/Support for Graphics, Molecular modelling


Peter J Stoehr

*name Summers,D.K.
From: DKS11
To: seqnet

I would like to participate in the European Directory.

My address:     DKS11@UK.AC.CAM.PHX
                David K. Summers
                Dept of Genetics
                Cambridge University
                Downing St
                Cambridge CB2 3EH

Interests:      Molecular biology of E. coli plasmids
                Site specific recombination
                DNA bending

*name Sussman,J.
From: CSJOEL@EARN.WEIZMANN
To: seqnet@UK.AC.CAM.PHX
Subject: electron mail address

Via:      UK.AC.RL.EARN; Sat, 09 Jan 88 19:03:49 GMT
Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 2246; Sat, 09
          Jan 88 19:03:49 GM
Received: from WEIZMANN.WEIZMANN.AC.IL by UKACRL.BITNET (Mailer X1.25) with
          BSMTP id 2244; Sat, 09 Jan 88 19:03:49 G
Received: by WEIZMANN (Mailer X1.25) id 5838; Sat, 09 Jan 88 21:03:04 +0200

in reply to your request:

I'm

Prof. Joel L. Sussman
Dept. of Structural Chemistry
Weizmann Institute of Science
Rehovot 76100  ISRAEL

CSJOEL@WEIZMANN   (Bitnet)

telephone 972-8-482638  or 972-8-483361

interest:

X-ray crystallography of DNA & Proteins
Cryogenic X-ray crystallography of Proteins & DNA
Protein & DNA model building & refinement
Structural studies of halophilic proteins

*name Winkler,H.
From: A8451DAB@EARN.AWIUNI11
To: SEQNET@UK.AC.CAM.PHX
Subject: Reply to your note on the BIONET bboard

Via:      UK.AC.RL.EARN; Mon, 11 Jan 88 09:34:11 GMT
Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 6998; Mon, 11
          Jan 88 09:34:11 GM
Received: from AWIUNI11.BITNET by UKACRL.BITNET (Mailer X1.25) with BSMTP id
          6995; Mon, 11 Jan 88 09:34:11 G
Received: by AWIUNI11 (Mailer X1.23b) id 1582; Mon, 11 Jan 88 10:35:01 MEZ

The yeast molecular genetics group at the Department of general
biochemistry at the University of Vienna is interested in participating
in your interest group. We are mainly working on the regulation of
expression of catalase in Saccharomyces cerevisiae. We do this by studying
effects on expression of mutations in the promoter region of catalase T
A second group in our lab is characterizing and purifying proteins that bind
to the upstream promoter region of catalase T.

My name is Hans Winkler and I am responsible for E-mail in our lab. The head
of our group and also head of the department in Prof. Dr. Helmut Ruis. Our
address is:

Inst. f. allgemeine Biochemie, Waehringerstr. 38, A-1090 Wien. Austria.

Our E-mail address is:   A8451DAB at AWIUNI11

                       Regards, Hans Winkler
Acknowledge-To: <A8451DAB@AWIUNI11>

MJB1@VMS-SUPP.CAM.AC.UK (01/16/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 59  C.RAWLINGS 15-JAN-1988 IUSC Workshop Expert Systems
From: Janet"C.RAWLINGS@UK.AC.CRC" <C.RAWLINGS@UK.AC.CRC> 15-JAN-1988 17:13
To: MJB1
Subject: IUSC Workshop Expert Systems


Date:  15-JAN-1988 17:06:38 GMT
From:  POST@UK.AC.CRC
To:  MJB1@UK.AC.CAM.VMS-SUPP
Sender: Janet"C.RAWLINGS@UK.AC.CRC" <C.RAWLINGS@UK.AC.CRC>
Reply-to: C.RAWLINGS@UK.AC.CRC
Subject: IUSC Workshop Handout

Received: from ICRF20 (not validated) by CRC; Fri 15 Jan 88 15:04:40-GMT
Date: Thu 14 Jan 88 14:16:30-GMT
From: Chris Rawlings <C-RAWLINGS%ICRF20@ICRF20>
Subject: IUSC Workshop Handout
To: mjb1%uk.ac.cam.vms-supp%JANET@CRC
Message-ID: <12366536977.32.C-RAWLINGS@ICRF20>


                      Expert Systems in Molecular Biology


                  IUSC Workshop on Molecular Biology Software
                   University of Cambridge 5-6 January 1988

                                 C.J. Rawlings

                         Imperial Cancer Research Fund
                                 P.O. Box 123
                             Lincoln's Inn Fields
                                London WC2A 3PX
                        Janet: C.RAWLINGS@UK.AC.MRC-CRC






EXPERT SYSTEMS
------ -------

Expert systems are programs designed to capture the skills of a  specialist  so
that  his  or  her  expertise  may be applied to a problem by a non-specialist.
Expert systems use IF-THEN rules as a  representation  of  the  problem-solving
skills  of  the specialist.  These rules are executed by an interpreter (called
the inference engine) that in many systems engages the user  in  some  sort  of
dialogue.   When  sufficient  information  has been obtained from the user, the
expert system will proffer its opinion.


SHELLS
------

Most expert systems are now built in programs called expert system shells.  The
shell is an expert system with no expertise.  It provides the rule language for
capturing the decision rules and the inference engine that drives the consulta-
tion  and  generates  conclusions  from  the  information provided by the user.
Shell commands  also  allow the user to interrogate the rules in the system and
support  simple  explanations  of  the  line  of  reasoning being followed (see
below).  Many of the commercial expert system shells are highly engineered  and
their  proponents  claim  that  it is possible for someone to start building an
expert system after only a couple of hours training.

EXPLANATION - The How and the Why
-----------   --- --- --- --- ---

An important feature of true expert systems that distinguishes them from  other
approaches   to  computer  assisted  decision-making  is  that  the  rule-based
representation of the specialists knowledge affords the possibility of generat-
ing  explanations  as to why a particular question is being asked or how a par-
ticular conclusion has been reached.

Although  relatively  crude,  when  used   appropriately,   these   explanation
facilities can make the program and the decisions it makes more accountable and
more intelligible to the non-specialist user.

KNOWLEDGE BASED SYSTEMS
--------- ----- -------

Expert systems are an example of the class of artificial intelligence  programs
called  knowledge  based systems. This style of programming emphasizes declara-
tive representations of human expertise but does not necessarily  restrict  the
representation  language  to   IF-THEN type rules and simple logical sentences.
Knowledge based systems are often large LISP or Prolog programs that use a par-
ticular  set  of  AI  techniques  to  realize  a  level  of competence at least
equivalent to the human specialists that normally perform the task.   The  sup-
port  tools for developing knowledge based systems are generally referred to as
toolkits rather than shells, since they provide a range of  representation  and
reasoning  methods  from  which  the developer may choose to fit the particular
application.  Where the toolkit does not support a  specialist  requirement  of
the  task  domain,  the  developer  has access to the underlying implementation
language (usually LISP, sometimes Prolog) to extend the toolkit.


KNOWLEDGE BASED SYSTEMS RESEARCH IN MOLECULAR BIOLOGY
--------- ----- ------- -------- -- --------- -------

Most of the existing research into the use of knowledge based method in molecu-
lar  biology  has used knowledge based systems rather than the more restrictive
expert systems.  The topics that have been addressed include the derivation  of
restriction  maps  from  restriction fragment data,[1] the automatic design and
debugging of gene cloning experiments,[2,3,4,5] (this research has lead to  the
development  of the commercial system from IntelliGenetics called STRATEGENE[6]
) advising on optimal sequencing  strategy  for  the  Maxam-Gilbert  method,[7]
simulation  of  gene  expression  and control,[8,9,10] solving the three dimen-
sional structure of proteins from NMR data,[11,12] and representing and reason-
ing about protein topology.[13]


EXPERT SYSTEMS IN MOLECULAR BIOLOGY
------ ------- -- --------- -------

It is generally agreed that expert systems techniques are well  suited  to  the
development  of  programs  that  either provide advice on a specialist topic or
solving classification problems such as those needed for fault diagnosis.  How-
ever,  it is also the case that todays expert systems shells do not provide the
computational power nor the representation techniques  required  for  molecular
sequence  data  analysis.  Nevertheless, there are other important and hitherto
relatively neglected areas of computer assistance for molecular biologists that
could be developed using present day expert systems.


In the Laboratory
-- --- ----------

As powerful computers become standard equipment in  molecular  biology  labora-
tories it will be possible to extend their use beyond the more obvious tasks of
data capture, storage and analysis and manuscript  preparation.   It  would  be
practical  to consider the development of expert systems to assist with a range
of laboratory-related tasks.  For example:


+    Advisory Expert Systems

     Expert systems could be used to provide  advice  on  topics  such  as  the
     selection  of  the best or alternative reagents (e.g. in buffers) or tech-
     nique to meet a particular experimental design constraint  such  as  cost,
     time  or  availability  of  reagents.  A commercially available example of
     such a program is Beckman's SPIN-PRO expert system that advises on aspects
     of  preparative  ultracentrifugation.   MAXAMIZE, [7] is a knowledge based
     system for advising on the  best  strategy  for  Maxam-Gilbert  sequencing
     strategies.

     One form that expert systems of this kind might take is an expert  labora-
     tory  notebook,  where  general  knowledge  and  advice  about techniques,
     reagents etc. could be mixed with the preferences that hold in the indivi-
     dual  laboratory.   Therefore  as  well  as providing supporting advice to
     existing members of the laboratory, the system(s) could be used  to  guide
     the newcomer in the ways of the lab.


+    Debugging Experimental Techniques

     For particularly complex experiments, or new techniques, or where  techni-
     cal expertise is limited to (typically) one member of a laboratory, expert
     systems could be developed to help diagnose  and  rectify  faults  in  the
     methods or reagents being used.


+    Transferring Expertise

     As the techniques of molecular biology become applied  in  more  and  more
     laboratories,  the  availability of skilled personnel can often be a prob-
     lem.  Expert systems could be used to complement  written  description  of
     methods  or  as part of computer aided instruction (CAI) systems  intended
     to transfer expertise out from the innovating laboratories to the rest  of
     the community.


Assisting Data Analysis
--------- ---- --------

Although present day expert systems are inadequate for most molecular  sequence
analyses, they could be used to augment existing analysis software.  These sys-
tems would probably require the more sophisticated representation techniques of
knowledge  based  system  development  tools,  rather than simple expert system
shells.


+    Selecting the Best Analysis Methods

     An important part of the  expertise of a sequence analysis  specialist  is
     translating  the  biological  question raised by some data into terms that
     can be solved using the algorithms and programs  available  on  the  local
     computer  system.  This involves knowing which techniques to apply  to the
     data (i.e. which programs to run) in  what  order  and  how  to  interpret
     and/or  modify  the results of one analysis before applying the next.  For
k can be daunting  and  it
     is  often the case that anyone with particular skills in sequence analysis
     gets inundated with requests from colleagues to assist or to perform  ana-
     lyses  on their behalf.  The role of sequence analysis advisor is one that
     is well suited to implementation using an expert system.  This problem  is
     largely  equivalent  to providing intelligent assistance for a statistical
     analysis package and the GLIMPSE project at Imperial College has  recently
     successfully used an expert system to develop a front-end to GLIM.

+    Making Better Use of Resources

     A potentially important factor in selecting the best data  analysis  stra-
     tegy is to minimize the computing resources required.  This issue could be
     separated from the scientific requirements  of  determining  the  analysis
     strategy or it could be an integrated part of it.

+    Tuning an Algorithm

     Making the optimum use and correctly interpreting the results of the  more
     complex  sequence  analysis  programs  such as those that perform sequence
     alignment and protein structure prediction requires some understanding  by
     the  user  of  the theoretical underpinnings of the algorithm employed and
     occasionally of the way it is implemented as a program.  Such  skills  are
     not  yet  common  amongst  laboratory  scientists  and therefore it is not
     unheard of for a scientist to abdicate all judgement to the results  of  a
     computer  program  without  understanding  its behaviour.  More often than
     not,  the behaviour of these types of programs is controlled by a  set  of
     numerical  parameters  that  tune the algorithm.  It is also the case that
     tuning can profoundly alter the results of an analysis.  Without  a  clear
     understanding  of  how  each  parameter affects the behaviour of the algo-
     rithm, the user cannot use the method properly.  Tuning sequence  analysis
     algorithms   requires knowledge and expertise and could be supported using
     an expert system or knowledge based  approach.

+    Intelligent Front Ends

     Some programs are notoriously difficult to  use  or  require  considerable
     experience  before meaningful results can be generated. It is the function
     of a front-end program to insulate the user from the idiosyncrasies of the
     offending software.  Intelligent Front Ends (IFEs) use expert system tech-
     niques to represent the knowledge required to run a program as well as the
     skills that  a specialist would apply when using the program.  The GLIMPSE
     expert system front-end to the statistical package GLIM is a good  example
     of an IFE.

     Whilst there are likely to be a number of sequence analysis programs  that
     might  qualify  for  an  IFE to help the novice or occasional user, an IFE
     might also help a molecular biologist  use  a  piece  of  general  purpose
     software  (e.g.  a  database management system) by tailoring the system to
     her likely requirements.  An IFE such as this could be  of  any  arbitrary
     sophistication,  from  simply  supporting  familiar terminology to a fully
     interactive system that solicits the users requirements in order  to  con-
     figure a database system.


FUTURE POSSIBILITIES FOR KNOWLEDGE BASED SYSTEMS
------ ------------- --- --------- ----- -------

Although research into knowledge based methods for molecular  biology  is  res-
tricted to relatively few centres, the interest is increasing.  Areas that have
not yet been extensively studied, but where research has begun include predict-
ing protein structure from amino acid sequence[14] and protein  modelling.

A consideration of developments in  the  way  that  scientists  are  using  the
rapidly  growing  DNA  sequence data libraries and the expectation that routine
exhaustive similarity searches will soon be possible using non-Von Neumann com-
puter architectures reveals that a problem will arise in sifting and interpret-
ing the results.   As the data libraries grow ever larger, the use of a  thres-
hold  value  to select interesting alignments based on a similarity metric will
become less practical since there is a conflict between selecting  a  realistic
number of hits for further analysis (increasing the threshold) and reducing the
threshold to include potentially interesting, but marginally significant align-
ments.   This  problem arises because the statistical significance of an align-
ment does not always predict biological significance.   It  should  however  be
possible  to  employ knowledge based techniques to allow a lowered threshold to
admit a large number of potentially significant alignments  with  a  subsequent
intelligent  filtering and partial interpretation of the results before presen-
tation to the scientist.


References
----------


1.   Stefik, M., "Inferring DNA Structures from Segmentation Data,"  Artificial
     Intelligence, vol. 11, pp. 85-114, 1978.

2.   Stefik, M., "Planning  with  Constraints  [MOLGEN:  Part  1],"  Artificial
     Intelligence, vol. 16, pp. 111-140, 1981.

3.   Stefik, M., "Planning and meta-planning   [MOLGEN:  Part  2],"  Artificial
     Intelligence, vol. 16, pp. 141-169, 1981.

4.   Friedland, P., Kedes, L., Brutlag, D.L., Iwasaki, Y.,  Bach, R., "GENESIS:
     a Knowledge Based Genetic Engineering Simulation System for Representation
     of Genetic Data and Experiment Planning ," Nucleic  Acids  Research,  vol.
     10, pp. 323-340, 1982.

5.   Bach, R.,  Iwasaki, Y.,  Friedland, P., "Intelligent computational  Assis-
     tance  for Experiment Design," Nucleic Acids Research, vol. 12, pp. 11-29,
     1984.

6.   Abarbanel, R.M., Bonura, T., Smith, D.H., "STRATEGENE, A Cloning  Worksta-
     tion  and  Librarian,"  Proceedings  of  AI  Biomed  1986, pp. 1-17, CRIM,
     Montpellier, France, 1986.

7.   Bach, R., Friedland, P.,  Brutlag,  D.L.,  Kedes,  L.,  "MAXAMIZE:  A  DNA
     Sequencing  Strategy  Advisor,"  Nucleic Acids Research, vol. 10, pp. 295-
     304, 1982.

8.   Meyers,  S.,  Friedland,  P.,  "Knowledge-based  Simulation   of   Genetic
     Regulation  in Bacteriophage lambda," Nucleic Acids Research, vol. 12, pp.
     1-9, 1984.

9.   Koton, P.A., Towards a Problem Solving System for Molecular Genetics,  MIT
     Laboratory of Computer Science; Technical Report MIT/LCS/TR-338, 1985.

10.  Sabey Weld, D., Switching Between Discrete and Continuous  Process  Models
     to  Predict  Genetic  Activity,  MIT  Artificial  Intelligence Laboratory;
     Technical Report 793.

11.  Hayes-Roth, B., Buchanan, B.G., Lichtarge, O.,  Hewett,  M.,  Altman,  R.,
     Brinkley, J., Cornelius, C., Duncan, B., Jardetsky, O., "PROTEAN: Deriving
     Protein Structure from Constraints," Proceedings of  American  Association
     of Artificial Intelligence, vol. 5, pp. 904-909, 1986.

12.  Freyman, F., "PROTO: An Approach for Determining Protein  Structures  from
     NMR  Data:  An Exercise in Large Scale Interdependent Constraint Satisfac-
     tion," Proceedings of AI Biomed  1986,  pp.  122-143,  CRIM,  Montpellier,
     France, 1986.

13.  Rawlings, C.J., Taylor, W.R., Nyakairu, J., Fox,  J.,  Sternberg,  M.J.E.,
     "Reasoning  about  protein  topology  using the logic programming language
     PROLOG," Journal of Molecular Graphics, vol. 3, pp. 151-157, 1985.

14.  Rawlings, C.J., Analysis and Prediction of Protein Structure using Artifi-
     cial  Intelligence,  Proceedings:   4th European Seminar in Computer Aided
     Molecular Design, IBC Press, 1987.
-------

MJB1@VMS-SUPP.CAM.AC.UK (01/16/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 60  From:  SEQNET  15 Jan 88  European list: A FORM TO FILL
Date: 15 Jan 88
From: SEQNET
Subject: European list: A FORM TO FILL

The response to the request for names, addresses and interests has been
good.  Before we go any further - Rob Harper suggests we use a standard
form which can be processed by computer.  So here it is along with the
latest batch of entries (in the old sloppy format).
Please keep sending your details so that we can make an effective list.
Thanks. Martin Bishop.


From: <HARPER@EARN.FINFUN> 15-JAN-1988 12:07
To: MJB1
Subj: NETWORK ID's and much much more...


Via:           UK.AC.RL.EARN; Fri, 15 Jan 88 12:06:20 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 7193; Fri, 15
               Jan 88 12:06:20 GM
Received:      from FINFUN.BITNET (HARPER) by UKACRL.BITNET (Mailer X1.25) with
               BSMTP id 7192; Fri, 15 Jan 88 12:06:19 G
Date:          Fri, 15 Jan 88 14:07 O
From:          <HARPER@EARN.FINFUN>
Subject:       NETWORK ID's and much much more...
To:            mjb1@UK.AC.CAM.VMS-SUPP
X-Original-To: mjb1@vms-supp.cam.ac.uk, HARPER

EXPERIMENTAL DATABASE

I like the idea that you are collecting NETWORK address's,
and I think that the folks at BIOTECH have similar plans in
the pipeline... and hopefully the data will be available on
BIOSERVE@UMDC. It is good that this type of information is
FREELY available to other users who may have similar professional
interests, and hopefully it will foster both national  and
international  contacts. I was most pleased to receive the names
and address's that came over the EARN network this morning, but
I have one small quibble, namely the information could be more
standardised and structured so I could make a very useful database
out of it here on my micro...

Since the possibilities for electronic communication is expanding, I
also think that it would be good if many different means of
communication could be listed; postal address, phone, telex, telefax
and network ID's etc.

People hate filling in forms and when they do fill them in they
do it all wrong anyway... so I am now going to give you THREE forms
which might be used for filling in useful and NONSENSITIVE information.
A BLANK form to add your OWN  data  according  to the examples
in the GENERAL and SPECIFIC guidlines.

Here they are for your consideration.

                                   BLANK FORM
NAME:          !                                                     !
ADDRESS:       !                                                     !
CITY:          !                                                     !
COUNTY:        !                                                     !
COUNTRY:       !                                                     !
PHONE:         !                                                     !
TELEX:         !                                                     !
TELEFAX:       !                                                     !
NETWORK IDS:   !                                                     !
PROFESSION:    !                                                     !
CAREER:        !                                                     !
GENERAL:       !                                                     !
       (the ! mark is only there as a guide line to keep things neat)

                                   GENERAL FORM
NAME:          Proper name (EARN/BITNET/JANET/ID Country)
ADDRESS:       Institution, Department
CITY:          Postal code, City
COUNTY:        County
COUNTRY:       Country
PHONE:         International code, citycode, Workphone (Homephone)
TELEX:         Telex number (Country)
TELEFAX:       Telefax number (Country)
NETWORK IDS:   JANET, BITNET, EARN
PROFESSION:    Job (particular expertise)
CAREER:        Interests
GENERAL:       Interests

                                  SPECIFIC FORM
NAME:          Robert Harper (HARPER@finfun FINLAND)
ADDRESS:       University of Helsinki, Department of Microbiology
CITY:          SF-00710 HELSINKI 71
COUNTY:         ---------------------------
COUNTRY:       FINLAND
PHONE:         +358 0 378011/466 (work) 308627 (home)
TELEX:         124 690 UNIH SF  (FINLAND)
TELEFAX:       374 1520
NETWORK IDS:   HARPER@finfun
PROFESSION:    Microbiologist (Lactobacillus research and fermentation)
CAREER:        Biotechnology  and Information Technology.
GENERAL:       Sleeping, Gardening, Public Domain software.

If I received the information in such a format it would be easy to
put it into a datbase file and do all sorts of nice things with it.

Rob "don't put crazy long messages out over the network" Harper

(Message number 7)    [ u ]
Accepted:  17:53:59 15 Jan 88
Submitted: 17:53:38 15 Jan 88
IPMessageId: -unspecified-
From: MJB1@UK.AC.CAM.VMS-SUPP
To: SEQNET@UK.AC.CAM.PHX

*name Ashburner,M.
From: MA11
To: seqnet
Subject: european directory

Michael Ashburner
Department of Genetics
University of Cambridge
Downing Street
Cambridge
England
Telephone 44-(0)223-333969
ma11@uk.ac.cam.phx
ashburner@arpa.bionet-20

*name Blair,G.E.
3   BCH6GEB@UK.AC.LEEDS.CMS1
    BCH6GEB%LEEDS.CMS1@EARN.RL.AC.UK

    Dr G Eric Blair,  Department of Biochemistry,
       University of Leeds,  Leeds LS2 9JT, U.K.

    Interests: eukaryotic transcription
               transcription factors & their interaction with DNA
               oncogenic transformation of mammalian cells
               molecular biology of human adenoviruses
               myelin gene expression


*name Herries,D.G.
From: BCH6DGH@UK.AC.LEEDS.UCS.CMS1
To: SEQNET@UK.AC.CAM.PHX


In connection with SEQNET bulletin no.52,  8.1.88
herewith 3 names for inclusion in Mol. Biol. interest list:


1   BCH6DGH@UK.AC.LEEDS.CMS1
    BCH6DGH%LEEDS.CMS1@EARN.RL.AC.UK

    Dr David G Herries,  Department of Biochemistry,  University of Leeds,
       Leeds LS2 9JT, U.K.

    Interests: computer applications in biochemistry



*name Jackman,P.J.H.
From: JACKMAN@UK.AC.AFRC.FRIN
To: mjb1@UK.AC.CAM.PHX

Re European Directory

Jackman@UK.AC.AFRC.FRIN
Dialcom 42:CDT0013

Dr.Peter J.H.Jackman
National Collection of Yeast Cultures,
AFRC Inst of Food Research,
Colney Lane,
Norwich, NR4 7UA
Norfolk,
UK

Curator National Collection of Yeast Cultures &  National Collection of Food
Bacteria.
Member committee Society for General Microbiology Computer Club,
Member committee Microbial Strain Data Network
interests molecular systematics,computing in microbiology,strain databases


*name McFerran,N.V.
From: ABJA1248@UK.AC.QUEENS-BELFAST.CENTRE.VAX1 15-JAN-1988 10:47
To: MJB1
Subj:


Date:  15-JAN-1988 10:46:34 GMT +01:00
From:  ABJA1248@UK.AC.QUEENS-BELFAST.CENTRE.VAX1
To:  MJB1@UK.AC.CAM.VMS-SUPP

Martin

Here is my E-Mail address at Queen's, for the list of European Mol. Biols.:

       ABJA1248@UK.AC.QUEENS-BELFAST.CENTRE.VAX

sorry it seems a bit of a mouthfull, the postal one isn't much better:

        Dr. N.V.McFerran
         Department of Biochemistry
         The Queen's University of Belfast
         Medical Biology Centre
         97 Lisburn Rd.
         BELFAST  BT9 7BL
         N. Ireland.

Interests include struct/fn relationships in proteins, notably proteases
          & dehydrogenases, image analysis applications & lab automation.

Many thanks for the organisational effort last week, all the best for '88.

Neil McFerran.

*name Millner,P.A.
2   BCH6PAM@UK.AC.LEEDS.CMS1
    BCH6PAM%LEEDS.CMS1@EARN.RL.AC.UK

    Dr PauL A Millner,  Department of Biochemistry,  University of Leeds,
       Leeds LS2 9JT, U.K.

    Interests: signal transducing proteins
               plant molecular biology


*name Saccone,C.
From: <SACCONE%VAXBA0.INFNET@EARN.IBOINFN> 15-JAN-1988 15:44
To: MJB1
Subj: EUROPEAN LIST


Via:           UK.AC.RL.EARN; Fri, 15 Jan 88 15:37:46 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 5088; Fri, 15
               Jan 88 15:37:46 GM
Received:
              from IBOINFN.BITNET by UKACRL.BITNET (Mailer X1.25) with BSMTP id
               5085; Fri, 15 Jan 88 15:37:44
Date:          Fri, 15 Jan 88 16:32 N
From:          <SACCONE%VAXBA0.INFNET@EARN.IBOINFN>
Reply-To:      <SACCONE%VAXBA0.INFNET@EARN.IBOINFN>
Subject:       EUROPEAN LIST
To:            MJB1@UK.AC.CAM.VMS-SUPP
X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK"

Message-id: <6515>
Date: FRI, 15-JAN-88 16:31 N
From: <SACCONE@VAXBA0.INFNET>
Reply-To: <SACCONE%VAXBA0.INFNET@IBOINFN.BITNET>  (alternate reply)
Subject: EUROPEAN LIST
To:   <MJB1@VMS-SUPP.CAM.AC.UK>
X-Original-To:  MJB1@VMS-SUPP.CAM.AC.UK, SACCONE

(1) SACCONE@VAXBA0.INFNET
(2) CECILIA SACCONE
    Dipartimento di Biochimica e
    Biologia Molecolare
    Universita' di Bari
    Via Amendola 165/A
    70126 - BARI (ITALY)
(3) Nucleic acid and protein database
    Computer application on nucleic acid sequences
    Molecular evolution
    Mitochondrial Biogenesis

*name Touzel,J.P.
From: Touzel@EARN.FRINRA72
To: seqnet%cam.phx@UK.AC.RL
Subject: Address List for Europe

Via:   UK.AC.RUTHERFORD.EARN ;  Fri, 15 Jan 88 08:44 GMT
        (V38 at UK.AC.RUTHERFORD.GEC-B)
Via:      UK.AC.RL.EARN; Fri, 15 Jan 88 08:44:18 GMT
Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 5966; Fri, 15
          Jan 88 08:44:18 GM
Received: from FRINRA72(TOUZEL) by UKACRL (Mailer X1.25) id 5964;
          Fri, 15 Jan 88 08:44:17 GM


   I would like to participate and to enter your mail list.

Electronic mail address : Touzel at FRINRA72 (EARN)
Name : Jean Pierre TOUZEL
Postal address : INRA, Station de Technologie Alimentaire,
                 B.P. 39,
                 F-59651 Villeneuve d'Ascq Cedex (France)
Interests : Methane bacteria, Formate dehydrogenase cloning

*name Van Leuvan, Fred
From: FRED@EARN.BLEKUL13
To: SEQNET  <SEQNET@UK.AC.CAM.PHX>
Subject: INFO

Via:      UK.AC.RL.EARN; Fri, 15 Jan 88 12:05:18 GMT
Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 7131; Fri, 15
          Jan 88 12:05:18 GM
Received: from BLEKUL13(MAILER) by UKACRL (Mailer X1.25) id 7129;
          Fri, 15 Jan 88 12:05:17 GM
Received: by BLEKUL13 (Mailer X1.24) id 2467; Wed, 13 Jan 88 13:45:47 CET

PLEASE KEEP ME POSTED ON ANY DEVELOPMENTS I,N THE FIELD OF MOLECULAR
BIOLOGY.MY POSTAL ADDRESS IS
             FRED VAN LEUVEN
             DEPT OF HUMAN GENETICS -UNIV OF LEUVEN
             GASTHUISBERG ON6
             B3000 LEUVEN BELGIUM.
Acknowledge-To: <FRED@BLEKUL13>

MJB1@VMS-SUPP.CAM.AC.UK (01/17/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 61  hazeldine@embl  16 Jan 88  EMBL NetServ - Further information
Date: 16 Jan 88
From: hazeldine@embl
Subject: EMBL NetServ - Further information
Postal-address: Meyerhofstrasse 1, 6900 Heidelberg, W. Germany
Phone:          +49 (6221) 387-0 [switchboard]


                EMBL NETWORK FILE SERVER - FURTHER INFORMATION
                ==============================================

Several people have been experiencing problems in using the file server
facility;  our initial announcement was clearly not explicit enough!

Please note that the following three restrictions currently apply:

1.   The machine from which you communicate with the server MUST be
     a BITNET/EARN node - the server is not accessible via gateways
     from any other network

2.   You MUST use the "interactive send" command, or its equivalent on
     your own machine, to communicate with the server - you cannot
     use a standard mail program

3.   You MUST send the file server a command as a one line message -
     it cannot process commands contained in files

We hope to enhance the file server software in the future to remove
these restrictions, and will of course inform you about any such developments.

In the meantime, if you have any questions or problems we suggest that you
contact your local computer service, or, if they cannot help, the EMBL
Data Library:

     EMBL Data Library          Telephone       : (06221) 387409
     Postfach 10.2209           Telefax         : (06221) 387306
     6900 Heidelberg            Telex           : 461613 (embl d)
     West Germany               Computer network: datalib@embl (BITNET/EARN)

MJB1@VMS-SUPP.CAM.AC.UK (01/19/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 62  From:  SEQNET  19 Jan 88  Common Data Submission Policy
Subject: Common Data Submission Policy
From: SEQNET
Date: 19 Jan 88

               COMMON DATA SUBMISSION POLICY

The major Nucleic Acid and Protein Sequence Database Centres have agreed a
common data submissions policy.  Under this policy, data submitted to any one
of the participating members will be shared by all others.  As submitted data
will be directly transmitted by the databases, research scientists need submit
data to only one of these groups.

The groups are:
GenBank Genetic Sequence Data Bank (GENBANK)
genbank%arpa.bionet-20@uk.ac.rl.earn

European Molecular Biology Laboratory (EMBL)
datasubs%embl@uk.ac.rl.earn

DNA Data Bank of Japan (DDBJ)
National Institute of Genetics

National Biomedical Research Foundation (NBRF-PIR)
Protein Information Resource
pirsub%gunbrf@uk.ac.rl.earn

Martinsreid Institute for Protein Sequence Data (MIPS)
Max Planck Institute for Biochemistry
mips%dm0mpb51@uk.ac.rl.earn

International Protein Information Database in Japan (JIPID)
Science University of Tokyo

Please fill in the forms provided for submitting your entry.
A program to aid proper completion of forms is expected soon.
===============================================================================
  Your name
 ------------------------------------------------------------------------------
  Organization
 ------------------------------------------------------------------------------
  Address



 ------------------------------------------------------------------------------
  Telephone                     Computer network address
 ==============================================================================
  On what medium and in what format are you sending your sequence data? (see
  end of this form for instructions)
      [ ] magnetic tape: density   [ ] 800  [ ] 1600   [ ] 6250
                         character code  [ ] ASCII  [ ] EBCDIC
                         record length ______________ blocksize ______________
                         label type _________________
      [ ] electronic mail
      [ ] diskette: computer ________________ operating system _______________
      [ ] printed copy
===============================================================================


CITATION INFORMATION

===============================================================================
  These data will be published by
  authors
 ______________________________________________________________________________
  title of paper
 ______________________________________________________________________________
  journal
 ------------------------------------------------------------------------------
  vol, pages,year (if known)
 ==============================================================================
  Does the sequence which you are sending with this form include data that
  does not appear in the above journal article?
     [ ] yes, beginning at base number _____ and ending at base _____   [ ] no
  How should this data be cited in the database?
     authors
 ------------------------------------------------------------------------------
     title of paper (if applicable)
 ------------------------------------------------------------------------------
     journal (if applicable)                       vol,pages,year
 ==============================================================================
  Please list references to papers and/or database entries which report
  sequences overlapping with data submitted here.
 ------------------------------------------------------------------------------
     first author     journal, vol., pages, year OR database, accession number
 ------------------------------------------------------------------------------

 ------------------------------------------------------------------------------

 ==============================================================================


DESCRIPTION OF SEQUENCED SEGMENT

Where appropriate, please use standard nomenclature or conventions. NOT ALL
QUESTIONS ARE RELEVANT TO ALL SEQUENCES.
===============================================================================
 What kind of molecule does this sequence represent?

  [ ] genomic DNA                                      [ ] tRNA
  [ ] organelle DNA (please specify) ______________    [ ] rRNA
  [ ] cDNA                                             [ ] snRNA
  [ ] other nucleic acid __________________________    [ ] scRNA

  [ ] peptide
      sequence assembled by  [ ] overlap of sequenced fragments
                             [ ] homology with related protein sequence
                             [ ] other (please specify) _____________________
-------------------------------------------------------------------------------
 length of sequence          [ ] bp   or   [ ] amino acid residues
-------------------------------------------------------------------------------
 library (type, name)                      clone(s)
-------------------------------------------------------------------------------
 genomic location/map position             gene name(s) (e.g., lacZ)
-------------------------------------------------------------------------------
 gene product name(s) (e.g., beta-D-galactosidase) and Enyme Commission number

-------------------------------------------------------------------------------
 source organism (Latin name) (e.g., Mus musculus)
-------------------------------------------------------------------------------
 strain (e.g., BALB/c)                     haplotype
-------------------------------------------------------------------------------
 tissue/cell line source                   [ ] germ line     [ ] rearranged
===============================================================================


FEATURES OF THE SEQUENCE

Please list below the first and last base/residue numbers of all significant
features identified within the sequence.  In the column marked "id," indicate
the method by which the feature was identified (E = experimentally; S = by
similarity with another sequence; C = match to an established consensus
sequence).  For nucleotide sequences, indicate (by writing an x in the column
marked "comp") if the feature is encoded by the strand complementary to that
reported here.

Some examples of significant features are:

  - regulatory signals (e.g., promoters, attenuators, enhancers)
  - transcribed regions (mRNA, rRNA, tRNA, etc.)
  - regions subject to post-transcriptional modification (e.g., introns,
    modified bases)
  - translated regions
  - extent of signal peptide, prepropeptide, propeptide, mature peptide
  - sites subject to post-translational modification (glycosylation,
    phosporylation)
  - other domains/sites of interest (e.g., extracellular domain, DNA-binding
    domain, active site, inhibitory site)
  - sites involved in bonding (disulfide, thiolester, intrachain, interchain)
  - regions of alpha helix or beta pleated sheet

================================================================================
   Numbering for features on the sequence you are submitting to us
       [ ] starts at 1   OR    [ ] starts at _______
   Does the numbering match that in your manuscript?   [ ] yes   [ ] no
--------------------------------------------------------------------------------
                   feature                    from       to       id     comp
------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

------------------------------------------- --------- ---------  ----- ---------

================================================================================



KEYWORDS

===============================================================================
Describe the properties of the sequence in terms of its associated
phenotype(s), the biological/enzymatic activity of its product and the general
functional classification of the gene and/or gene product.  Also indicate
macromolecules which the gene product can bind (e.g., DNA; Ca++; other
proteins), subcellular localization of the gene product and any other
information you think is relevant.

EXAMPLE (for the viral erbB gene sequence): transforming capacity;
EGF receptor-related; transmembrane protein; tyrosine kinase; oncogene.
-------------------------------------------------------------------------------



===============================================================================

MJB1@VMS-SUPP.CAM.AC.UK (01/28/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 66  Julie_Glanville@NEWCASTLE  27 Jan 88  Bacillus licheniformis geno
From: Julie_Glanville@UK.AC.NEWCASTLE
To: seqnet@UK.AC.CAM.PHX
Subject: Bacillus licheniformis genome

Does anyone have or know of a gene bank containing the
Bacillus licheniformis genome in an E.coli or B.subtilis vector,
which they would be willing to share?
Many thanks

Colin R. Harwood
Dept. Microbiology
Univ. of Newcastle upon Tyne, UK
JANET: mma4@ncl.mts
Bulletin_# 65  From:  SEQNET  28 Jan 88  More European Molecular Biologists
From: SEQNET
Subject: More European Molecular Biologists
Date: 28 Jan 88


From: BARCLAY@UK.AC.OXFORD.VAX 19-JAN-1988 17:31
To: MJB1
Subj:


Date:  19-JAN-1988 17:29:59 GMT
From:  BARCLAY@UK.AC.OXFORD.VAX
To:  MJB1%UK.AC.CAM.VMS-SUPP@UK.AC.CAM.VMS-SUPP

Dear Martin Bishop,
                Thank you for the mail and putting us on
the Bionet Seqnet and Biotech networks. THey look
as if they will be helpful.
                Congratulations on organising such
an interesting IUSC workshop in Cambridge.
           Yous Sincerely
              A. Neil Barclay
*name Coulson,A.F.W.
NAME:          A.F.W.Coulson@uk.ac.edinburgh (JANET)
ADDRESS:       Dept of Molecular Biology, Univ of Edinburgh
CITY:          King's Buildings, Mayfield Rd,  Edinburgh EH9 3JR
COUNTY:        !                                                     !
COUNTRY:       United Kingdom
PHONE:         031 667 1081 Ext 2723
TELEX:         727442 (UNIVED G)
TELEFAX:       !                                                     !
NETWORK IDS:   a.coulson@uk.ac.edinburgh
PROFESSION:    Joint Director, Biocomputing Research Unit
CAREER:        Computing for molecular biology, protein engineering,
                beta-lactamases
GENERAL:       !                                                     !
From: RAY@UK.AC.LEICESTER.VAX 19-JAN-1988 12:30
To: MJB1
Subj:


Date:  19-JAN-1988 12:16:16 GMT
From:  RAY@UK.AC.LEICESTER.VAX
To:  mjb1@UK.AC.CAM.VMS-SUPP

Details:-
Dr.Raymond Dalgleish,
Department of Genetics,
University of Leicester,
University Road,
Leicester LE1 7RH, U.K.
Tel 44 (0533) 523425
E-mail ray@uk.ac.le.vax

Interests:- Inherited human connective tissue disorders including Marfan
syndrome, osteogenesis imperfecta and the Ehlers-Danlos syndromes. I am co-
manager of the Molecular Biology Users Group (MBUG) on the VAX at Leicester.
(Message number 1)
Accepted:  16:44:27 20 Jan 88
Submitted: 10:50:22 20 Jan 88
IPMessageId: -unspecified-
From: ELDER@UK.AC.OXFORD.VAX
To: seqnet@UK.AC.CAM.PHX

NAME:          JK Elder
ADDRESS:       Department of Biochemistry, University of Oxford
CITY:          Oxford  OX1 3QU
COUNTRY:       UK
PHONE:         +44-(0)865-275228
TELEX:         83681 (UK)
NETWORK IDS:   JANET: elder@uk.ac.ox.vax
               EARN:  elder%ox.vax@earn.rl.ac.uk
GENERAL:       Automatic construction of restriction maps
               Automatic sequencing
               Image processing
               Molecular biology software which runs on Suns and/or under UNIX
(Message number 3)
Accepted:  15:02:44 26 Jan 88
Submitted: 12:19:05 26 Jan 88
IPMessageId: -unspecified-
From: BCH6DGH@ UK.AC.LEEDS.UCS.CMS1
To: seqnet@ UK.AC.CAM.PHX


In connection with SEQNET bulletin no.52,  8.1.88
herewith 1 more name for inclusion in Mol. Biol. interest list:


    DRBDH@UK.AC.LEEDS.BIOVAX
    DRBDH%LEEDS.BIOVAX@UK.AC.RL.EARN

    Dr B David Hames,  Department of Biochemistry,  University of Leeds,
       Leeds LS2 9JT, U.K.

    Interests: eukaryotic transcription
               molecular biology of development
               homeobox gene function in vertebrates
               Dictyostelium
               -------------
               Xenopus
               -------

(Message number 30)
Accepted:  17:10:34 25 Jan 88
Submitted: 11:53:17 25 Jan 88
IPMessageId: -unspecified-
From: FMI019@UK.AC.SOUTHAMPTON.IBM
To: mjb1@UK.AC.CAM.PHX


FROM:-   DR. J.E.HECKELS
         DEPARTMENT OF MICROBIOLOGY
         UNIVERSITY OF SOUTHAMPTON MEDICAL SCHOOL
         EMAIL:- FMI019@SOTON.IBM

    DEAR Dr. Bishop,
         I have read with interest recent articles in Binary concerning
the Seqnet bulletin board for molecular biologists. In this department
myself and several collegues are involved in cloning and sequencing the
surface proteins of a number of pathogenic bacteria and viruses. I feel
that we are not yet making fullest use of data and programmes which may
be available elsewhere. I would therefore be grateful if it were possible
for me to recieve the information on the seqnet bulletin board.
    I have also seen in Binary a list of molecular biology programmes
which are available for PCs and I would be grateful for any further
information if this has been updated recently.

    Thank you in advance for your help.
           Yours sincerely
             John Heckels
From: Andrew_T_Lloyd @ UK.AC.NEWCASTLE 20-JAN-1988 11:35
To: MJB1
Subj: Bulletins


Date:     Wed, 20 Jan 88 11:33:29 GMT
From:     Andrew_T_Lloyd @ UK.AC.NEWCASTLE
To:       mjb1 @ UK.AC.CAM.VMS-SUPP
Subject:  Bulletins

Greetings,
Can you put me on your mailing list for
SEQNET and all that Mol Biol chitchat
that I currently get via Julie Glanville
in Microbiology Newcastle?  I guess my
address will get appended by our computer
Regards, Andrew T. Lloyd, Genetics,
Newcastle.

*name LUCIANO MILANESI
(1) MILANESI@ICILVX.INFNET
(2) LUCIANO MILANESI
    Istituto di Tecnologie Biomediche
    Avanzate
    C.N.R.
    Via Ampere 56
    20133 - MILANO (ITALY)
(3) Nucleic acid and protein database
    Computer application on nucleic acid sequences









From: <WMBORMON@EARN.HLERUL52> 26-JAN-1988 11:16
To: MJB1
Subj: computer address list


Via:           UK.AC.RL.EARN; Tue, 26 Jan 88 11:15:44 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 5679; Tue, 26
               Jan 88 11:15:43 GM
Received:
           from HLERUL52.BITNET (WMBORMON) by UKACRL.BITNET (Mailer X1.25) with
               BSMTP id 5673; Tue, 26 Jan 88 11:15:42
Date:          Tue, 26 Jan 88 12:10 N
From:          <WMBORMON@EARN.HLERUL52>
Subject:       computer address list
To:            mjb1@UK.AC.CAM.VMS-SUPP
X-Original-To: mjb1@vms-supp.cam.ac.uk, WMBORMOND

Dear Dr. Bishop,
Thanks again for having us at the IUSC Symposium at such late notice.
I am glad that the computer address idea seems to catch on. I also
wish to thank you for putting me on the bulletin mailing list.
It has already provided us with
very useful information.
Please find my computer address according to the suggested
form. Best regards, Hans van Ormondt.

NAME:          Hans van Ormondt(EARN WMBORMOND@HLERUL52)
ADDRESS:       Sylvius Laboratories, Univ. of Leiden, P.O.Box 9503
CITY:          2300 RA Leiden
COUNTY:
COUNTRY:       The Netherlands
PHONE:         31 71 276034
TELEX:
TELEFAX:       31 71 276292
NETWORK IDS:   EARN
PROFESSION:    Biochemist
CAREER:        Gene therapy; DNA software
GENERAL:       AtariST


From: STA019 @ UK.AC.AFRC.SASS 21-JAN-1988 21:15
To: MJB1
Subj:


Date:     THU, 21 JAN 88 20:55:28 BST
From:     STA019 @ UK.AC.AFRC.SASS
To:       mjb1 @ UK.AC.CAMBRIDGE.VAX-VMS.SUPPORT


Address List

I would like to remain on the SEQNET mailing list.
electronic mail address :-  sta019  @ uk.ac.afrc.sass
        Graham Wetherill,
         Scottish Agricultural Statistics Service,
          King's Buildings, Mayfield Road,
           Edinburgh, UK,  EH9 3JZ
TEL: 031-667 1081 ext 2921   TELEX: 727442 (UNIVED G)   FAX: 031-667 7938
my initerests are in Statistical and computing support and related research.

MJB1@VMS-SUPP.CAM.AC.UK (01/30/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 67  reisner@au.oz.su.facet  28-JAN-1988  Transputers and Occam in Aus
From: reisner@au.oz.su.facet
Date: 28-JAN-1988
To: MJB1
Subject: Transputers and Occam in Australia


Received: from Ean.Ean-Relay.AC.UK by Ean-Relay.AC.UK   via EAN  id aa05029;
          28 Jan 88 18:50 GMT
Date: 28 Jan 88 18:04 BST
From: reisner@au.oz.su.facet
Dear Martin,

Below is the announcement which I thought might interest SEQNET users.
As you will see now mention of the Computing Surface.  I Think Meiko ought
to make their presence felt.

Cheers,
 Alex Reisner

**************************************************************************
Newsgroup: aus.general, Item: #345, Subject: Transputer & OCCAM Conference


Path: munnari!goanna!yabbie!gecko!rcojh
From: rcojh@gecko.rmit.oz (John Hulskamp)
Newsgroups: melb.seminars,aus.general
Subject: Transputer & OCCAM Conference
Keywords: Transputer, OCCAM
Message-ID: <366@gecko.rmit.oz>
Date: 13 Jan 88 02:48:14 GMT
Distribution: aus
Organization: RMIT Comm & Elec Eng, Melbourne, Australia.
Lines: 122



AUSTRALIAN
TRANSPUTER AND OCCAM USER GROUP
CONFERENCE & EXHIBITION

23 & 24 JUNE 1988

GLASSHOUSE THEATRE
ROYAL MELBOURNE INSTITUTE OF TECHNOLOGY
124 La Trobe Street
MELBOURNE AUSTRALIA

In conjunction with Hawk Electronics Pty. Ltd., the Centre for Advanced
Technology in Telecommunications within ing
transputers and to formally establish an Australian Transputer and OCCAM User
Group.


CALL FOR PAPERS

The Conference will focus on the latest developments in the transputer family,
the language support for transputer systems, and applications. Papers on such
developments are being solicited from interested persons. Persons wishing to
submit a contribution in the form of a paper and/or demonstration should
provide an abstract as soon as possible (and no later than 29 February 1988)
to the Conference Convenor, Mr John Hulskamp, at the address given below. Final
camera-ready papers should be provided on A4 paper, be no longer than 6 pages,
by 27 May 1988, in time for inclusion in a C

The all-inclusive Conference fee of $A195 will include morning, afternoon teas
and lunch on both days as well as a Conference Dinner.


EXHIBITION

In conjunction with the Conference, an exhibition will demonstrate the latest
equipment being developed with the transputer family. Persons and/or
organisations wishing to mount an exhibit are most welcome to apply, and discuss
their requirements with the Conference Convenor, Mr John Hulskamp.

Hawk Electronics Pty. Ltd will also provide a demonstration of the computer
graphics capabilities of the transputer family using an IBM PC/AT facility
incorporating multi-transputer boards.


USER GROUP

One outcome of the Conference will be the formal establishment of an Australian
Transputer and OCCr Lecturer within the
Digital Systems Group of the Department of Communication and Electronic
Engineering at the Royal Melbourne Institute of Technology. He may be contacted
as follows:

 Mr John Hulskamp,
 Department of Communication and Electronic Engineering,
 Royal Melbourne Institute of Technology,
 G.P.O. Box 2476V,
 MELBOURNE 3001  AUSTRALIA

 Telephone: (03)660-2453/2090
 e-mail: rcojh@gecko.rmit.oz


To indicate your interest in attending the Conference, contact the Conference
Convenor, Mr John Hulskamp, as above, or by
returning this portion of the Announcement.


Name:





Organisation:





Address:



Phone:



_____ I am interested in Attending the Conference



_____ I am interested in Presenting a Paper and/or Demonstration



_____ I am interested in mounting an Exhibit



_____ I am UNABLE to Attend the Conference but would like to be kept informed



_____ I am interested in participating in the Users Group

MJB1@VMS-SUPP.CAM.AC.UK (02/02/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 68  From:  SEQNET  1 Feb 1988  More european molecular biologists
Date: 1 Feb 1988
Subject: More european molecular biologists
From: SEQNET
JB86 29 Jan 1988 13.43
Martin,
Here's my details for the list of molecular biologists:

NAME:            John R. Beeching
ADDRESS:         Biological Sciences, University of Bath
CITY:            Bath BA2 7AY
COUNTRY:         UK
PHONE:           (0225) 826826 ext. 5193
TELEX:           44097 (UK)
NETWORK ID:      JANET: JB86@.UK.AC.CAM.PHX
PROFESSION:      Plant molecular biologist
INTERESTS:       Plant gene expression, RFLPs, plant tissue culture.

From: R.Bingham @ uk.ac.edinburgh 28-JAN-1988 14:46
To: MJB1
Subj: List of European molecular biologists.


Date: 28 Jan 88  14:45:16 gmt
From: R.Bingham @ uk.ac.edinburgh
Subject: List of European molecular biologists.
To: MJB1 @ uk.ac.cambridge.vax-vms.support
Message-ID: <28 Jan 88  14:45:16 gmt  040098@EMAS-A>

Please add me to your email list of European molecular biologists
(I already receive SEQNET/BIONET/BIOTECH bulletins, please do not
duplicate!)

Dr. Richard W. Bingham
Dept. of Veterinary Pathology
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Summerhall
Edinburgh EH9 1QH

email:  R.W.Bingham @ uk.ac.edinburgh
tel: 031-667 1011 Ext. 5281/5283
telex: 727442 (UNIVED G)
interests: molecular virology (particularly paramyxoviruses &
 papillomaviruses); computing

NAME  Rod Casey
ADDRESS  John Innes Institute, Colney Lane, Norwich,
  NR4 7HU, UK.
PHONE  (0603) 52571
TELEX  975122 JIINOR G
TELEFAX  (0603) 56844
NETWORK  CASEY@UK.AC.AFRC.JII
PROFESSION Biochemist
CAREER  Variation in the structure and synthesis of proteins
GENERAL  Molecular genetics. Protein structure and synthesis,
  especially seed proteins, including storage proteins,
  lectins, trypsin inhibitors and lipoxygenases.

(Message number 36)
Accepted:  09:59:36 30 Jan 88
Submitted: 09:37:25 29 Jan 88
IPMessageId: -unspecified-
From: Jean-Michel Claverie <JMC@EARN.PASTEUR>
To: Martin J. Bishop <MJB1@UK.AC.CAM.PHX>
Subject: seqnet file

Via:      UK.AC.RL.EARN; Sat, 30 Jan 88 02:07:19 GMT
Received: from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 8717; Sat, 30
          Jan 88 02:07:19 GM
Received: from CDC.ENS.FR by UKACRL.BITNET (Mailer X1.25) with BSMTP id 8716;
          Sat, 30 Jan 88 02:07:19 G
Received: from PASTEUR (MAILER) by CDC.ENS.FR (Mailer X1.24) with BSMTP id
          2583; Fri, 29 Jan 88 10:04:31 S

Hi there !

I hope everything is going smoothly in Great Brittany, as for rain, we certain
ly are even. Thanks for putting me on your mailing list and inviting me to your
IUSC workshop. Unfortunately, I was in the US at that time.
I do have a precise question so: would you know a Bitnet address for
Michael S. Waterman of Univ. Southern Calif. in LA ? Of course, I need to
join him about a special issue in Bull. Math. Biol. Do you intend to submit
a work to him ?
Finally here is my application to your BioInformatics name list:

NAME:          Jean-Michel Claverie
ADDRESS:       Computer Science Unit, Institut Pasteur, 28 rue Dr Roux
CITY:          75724 - PARIS, cedex 15.
COUNTRY:       FRANCE
PHONE:         (33)(1)45 68 85 10
TELEX:         250609F
TELEFAX:       (33)(1)43 06 98 35
NETWORK IDS:   JMC@PASTEUR
PROFESSION:    Head, Computer Science Unit, Institut Pasteur
CAREER:        General Biocomputing, sequence analysis, databank (PGtrans,
               PseqIP), molecular modelling, immunology, AIDS.
GENERAL:       Most active research: T-immunogenicity, AIDS, molecular modelling

HARWARE:       DATA GENERAL MV8000/10000, MicroVAXII, E&S PS390, PCs, MacInt.
LANGAGE:       FORTRAN77, C, PASCAL, ORACLE, INGRES.
SOFTWARE:      Complete Sequence Analysis (SASIP), Staden, PCgene, Lipman, ...
DATABANKS:     GenBank, EMBL, NBRF-PIR, PGtrans, PSD-Kyoto, Newat, PSeqIP,
               Swiss-Prot.
----

NAME: Prof. Peter T. Emmerson
ADDRESS: Dept. Biochemistry, University of Newcastle upon Tyne
CITY: Newcastle upon Tyne, NE2 4HH
COUNTY: Tyne and Wear
COUNTRY: UK
PHONE: 091-232-8511
TELEX: 53654
TELEFAX 091-261-1182
NETWORK ID: Janet: BIB3@UK.AC.NCL.MTS
CAREER: Interests: DNA repair. Genetic recombination. Molecular biology of
paramyxoviruses.


NAME: Dr. Colin R. Harwood
ADDRESS: Dept. Microbiology, University of Newcastle upon Tyne
CITY: Newcastle upon Tyne, NE2 4HH
COUNTY: Tyne and Wear
COUNTRY: UK
PHONE: 091-232-8511
TELEX: 53654
TELEFAX 091-261-1182
NETWORK ID: Janet: mma4@UK.AC.NCL.MTS
CAREER: Interests: Gene expression and protein export in gram positive
bacteria.


NAME:            DESMOND HIGGINS
ADDRESS:         TRINITY COLLEGE, DUBLIN 2. DEPARTMENT OF GENETICS
CITY:            DUBLIN
COUNTRY:         IRELAND
PHONE:           +353 1 772941 /1969
TELEX:           93782 TCD EI (IRELAND)
TELEFAX:         772694
NETWORK ID:      D.HIGGINS@IRL.HEA.TCD.DEC20
PROFESSION:      RESEARCH FELLOW
GENERAL:         DNA/PROTEIN SEQUENCE ANALYSIS AND DATABASES,
                 EVOLUTION, INSECT TAXONOMY.



NAME: Dr. Monica Hughes
ADDRESS: Dept. Genetics, University of Newcastle upon Tyne
CITY: Newcastle upon Tyne, NE2 4HH
COUNTY: Tyne and Wear
COUNTRY: UK
PHONE: 091-232-8511
TELEX: 53654
TELEFAX 091-261-1182
NETWORK ID: Janet: mma4@UK.AC.NCL.MTS
CAREER: Interests: Higher plant molecular genetics, stress responses, cyanide
metabolism.



NAME:            PAUL SHARP
ADDRESS:         TRINITY COLLEGE, DUBLIN 2.  DEPARTMENT OF GENETICS
CITY:            DUBLIN
COUNTRY:         IRELAND
PHONE:           +353 1 772941 /1035
TELEX:           93782 TCD EI (IRELAND)
TELEFAX:         772694
NETWORK ID:      P.SHARP@IRL.HEA.TCD.DEC20
PROFESSION:      LECTURER IN GENETICS
GENERAL:         DNA SEQUENCE ANALYSIS, MOLECULAR EVOLUTION,
                 CODON USAGE, HIV, YEAST, BACILLUS, UBIQUITIN.

MJB1@VMS-SUPP.CAM.AC.UK (02/03/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 69  From:  SEQNET  2 Feb 1988  Biocomputing Research in Europe
Date: 2 Feb 1988
From: SEQNET
Subject: Biocomputing in Research Europe

From: JF600@EARN.ALBNY1VX
To: tch2@UK.AC.CAM.PHX
Subject: From J.M.Carazo

Via:           UK.AC.RL.EARN; Mon, 25 Jan 88 12:23:44 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 5018; Mon, 25
               Jan 88 12:23:44 GM
Received:
              from ALBNY1VX.BITNET (JF600) by UKACRL.BITNET (Mailer X1.25) with
               BSMTP id 5015; Mon, 25 Jan 88 12:23:43
X-Original-To: tch2@phx.cam.ac.uk

To: TCH2%PHX.CAM.AC.UK@UCL-CS-MAILNET.MAILNET

To: TCH2%UK.AC.CAM.PHX@UCL-CS-MAILNET.MAILNET


Dr.T.C.Hodgman
MRC Laboratory of Molecular Biology
Cambridge
U.K.
                                              Dr.J.M.Carazo
                                              New York State Health Department
                                              Empire State Plaza
                                              Albany, NY, 12201
                                              (JF600@ALBNY1VX.BITNET)
Dear Dr.Hodgman,

I have heard of you through the bulletin #51 of the BIOTECH FORUM
in which you presented a Report on the IUSC Workshop.

As you may know, the Research Council of Spain
is organizing in Madrid a national biotechnology resource called
Centro Nacional de Biotecnologia. A Biocomputing Research Unit
has been created as part of this center and
I have been appointed as its Coordinator.

Currently the Unit is in a definition state. Both hardware and
software will be bought during the last half of this year and,
evidently, I am trying to get as much information as possible
about how other Biocomputing units are organized, which software
they use, which hardware have been found most suitable for each
application (and why), ... and a number of questions like that.

As you commented a number of times in your IUSC report, coordination
is a key issue in order to avoid duplications
and to enhance software compatibility.
In this context I would appreciate very much any kind of
information you could send me.
Particular topics I am interested in are

1) A list of the software used, both at the level of operating
systems and compilers (anybody using UNIX and C?), and at the level
of applications.

2) I inted to look at the hardware from the point of how good
is the implementation of the software that I really need in a
particular system architecture. I would then appreciate any suggestion
you might have about which hardware you stimate is better
for this application.

3) From your report I see that there are, at least, Biocomputing
Units (or something equivalent) in Edinburg and somewhrere in
Germany (I assume that besides the EMBL), Holland and Ireland.
Could you send me the addresses of the people in charge of
them? (electronic as well as postal, please).

4) Last but not least. Could you send me contact addresses of any
national or international comitee engaged in the coordination
of Biotechnology software? (and hardware, if any).

I really see that I am asking you too many things, I thank
you in advance for any help you might be able to give me.

Sincerely,..............................Jose Maria Carazo

====================================================================
Dear Dr.Carazo,

Dr. Hodgman has asked me, as organiser of the IUSC Workshop,
to reply to you.

I will also post your letter on the SEQNET Bulletin Board in the hope
that others at UK and European Centres will contact you.
SEQNET is a bulletin board for molecular biologists in Europe and operates
from Cambridge University (SEQNET@UK.AC.CAM.PHX).

In the UK there are many universities engaged in molecular biology
computing, though a fewer number are doing research into problems
of new techniques and algorithms.  Most centres use VAX/VMS and
the Staden, UWGCG and NBRF software for routine applications.
There are research groups, eg. at Oxford and ICRF using Unix on Suns.
There is an interest in parallel computing in Edingburgh.

In Cambridge, the University has a VAX 8350 running VMS and the MRC
Laboratory of Molecular Biology has a VAX 8600 also running VMS.
Unix is not much used.  There is a teaching laboratory with 7 IBM
PC AT machines and an IBM PS/2 Model 60 which are used for DNA
sequence analysis.  The PCs are connected to the VAX by an X.25
network, and an ethernet is planned.

As far as national and european organisation goes I suggest you contact
Biotechnology Directorate,
Science and Engineering Research Council,
Polaris House,
North Star Avenue,
Swindon SN2 1ET
UK

and
B.J.W.M. Niewenhuis
Commission of the European Communities
Division of Biotechnology
200 rue de la Loi
B-1049 Brussels
Belgium.

                                                   Yours sincerely,
                                                   Martin Bishop.
                                                   University of Cambridge
                                                   Computer laboratory
                                                   New Museums Site
                                                   Pembroke Street
                                                   Cambridge CB2 3QG
                                                   UK.
                                                   Tel. 0223-334732
                                  E-mail mjb1@uk.ac.cam.phx

MJB1@VMS-SUPP.CAM.AC.UK (02/04/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 70  From:  SEQNET@CAM.PHX  4 Feb 88  What is SEQNET?
Date: 4 Feb 88
From: SEQNET@CAM.PHX
Subject: What is SEQNET?

SEQNET Bulletin Board
Cambridge University, UK.

Dr. M.J. Bishop,
Computer Laboratory,
New Museums Site,
Pembroke Street,
Cambridge CB2 3QG
UK.
Telephone 0223-334732
JANET mail address MJB1@UK.AC.CAM.PHX

Dr. Michael Ashburner,
Department of Genetics,
Downing Street,
Cambridge CB2 3EH
UK.
Telephone 0223-333969
JANET mail address MA11@UK.AC.CAM.PHX

SEQNET is general Bulletin Board for Molecular Biologists  which was established
in November 1986 on the Phoenix/MVS Service running on the IBM 3084
at Cambridge University. The original purpose of this was to act as a
two-way service for molecular biologists within the UK academic community.
"Subscribers" both receive new Bulletins and submit new Bulletins for
widespread distribution via the UK Joint Academic Network (JANET).
SEQNET bulletins contain announcements of
meetings, of new software, of the availability of reagents and experimental
tricks, of requests for information, and many other matters.
Items included are of widespread
interest to the community, rather than being parochial to a particular
University or research group.

It is possible to read the bulletins by logging on to the Cambridge
computer.  This can be done over JANET or PSS which means that access
is possible from anywhere in the UK (a telephone socket, modem and
terminal are the minimum requirements).  Access is not restricted
to Universities and Polytechnics; industrial users are welcome.

Bulletins are also mailed over JANET.
Workers in the UK wishing to receive Bulletins need to
have access to a machine with the ability to receive mail via JANET.
Bulletins are, similarly, submitted via JANET  to Cambridge for
distribution to other sites.
These are distributed as they arrive, and no
form of "editorial control" is exercised.
However, there are restrictions on the use of JANET for commercial
purposes and the rules must be adhered to.
To send Bulletins for inclusion use the JANET address: SEQNET@UK.AC.CAM.PHX

SEQNET has set up reciprocal arrangements with other
Bulletin Boards so that we now distribute to the UK community
Bulletin Boards from BIONET and BIOTECH received from ARPANET and BITNET.

It soon became apparent that there was a need for distribution of
BIONET, BIOTECH and SEQNET bulletins in the European Community
and nearby countries.   We now distribute bulletins to workers in
Australia, Canada (via BIONET), Denmark, Eire, Finland, France,
Germany, Greece, Israel, Italy, Netherlands, UK and USA (via BIONET).
SEQNET acts as the forum for matters of European interest.

MJB1@VMS-SUPP.CAM.AC.UK (02/05/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 71  From:  HARPER@EARN.FINUH  4 Feb 1988  UPLOADING files
Date: 4 Feb 1988
From: HARPER@EARN.FINUH
To: seqnet@UK.AC.CAM.PHX
Subject: UPLOADING files

Via:           UK.AC.RL.EARN; Thu, 04 Feb 88 10:46:12 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 1238; Thu, 04
               Feb 88 10:46:12 GM
Received:
          from FINUH.BITNET (HARPER) by UKACRL.BITNET (Mailer X1.25) with BSMTP
               id 1237; Thu, 04 Feb 88 10:46:10
X-Original-To: seqnet@phx.cam.ac.uk, HARPER

           %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                    TITLE: HOT UPLOAD FINNISH STYLE
           %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    I  was  reading in BIONET that someone was having problems  with
    PROCOMM. It sounded that the excess characters where coming from
    a noisy phoneline. PROCOMM has the ability to UPLOAD texts which
    you have prepared off line... which is perhaps the best to enter
    sequence  data.   The  PG  UP  key  will  give  you  a  list  of
    possibilities... for texts like this one I am writing now choice
    #7 (ascii/upload) should put the prepared text in with few or no
    errors.  If  you  want accuracy (CRC) error  checking  then  the
    choice  would  be  KERMIT...  but now for  something  completely
    different!!!!!

    Here   is something to make your lives easy...  a simple  method
    for uploading onto bulletin boards,  or E-mail scratchpads.  The
    method  involves using SIDEKICK to  PASTE things  straight  into
    your work area. Here are the instructions.

    1 Open the SIDEKICK Notepad.
    2 Write your text
    3 Mark the beginning of the text with CTRL K B
    4 Mark the end of the text with CTRL K K
    5 Set the BLOCK to be PASTED with CTRL K E
    6 When asked "Press key to paste with" select function key F5
    7 When asked BLOCK or LINE mode choose B for BLOCK
    8 Hit ESC to get out of SIDEKICK
    9  Get to the place where you want to add a message, and  wait
    for  the the system to tell you to enter text.
    10  Hit   the   function key F5 and the text  will   appear   in
    your scratch pad.

Simple and very effective...  highly recommended. You  need  SIDKICK
v 1.5 onwards,  older versions don't  have  the PASTE facility.

-=ROB=-

==============
(Message number 6)
Accepted:  11:52:00 05 Feb 88
Submitted: 13:04:00 04 Feb 88
IPMessageId: -unspecified-
From: HARPER@EARN.FINUH
To: seqnet@UK.AC.CAM.PHX
Subject: We are "backwards" in Finland

Via:           UK.AC.RL.EARN; Thu, 04 Feb 88 11:06:45 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 2591; Thu, 04
               Feb 88 11:06:44 GM
Received:
          from FINUH.BITNET (HARPER) by UKACRL.BITNET (Mailer X1.25) with BSMTP
               id 2526; Thu, 04 Feb 88 11:06:37
X-Original-To: seqnet@phx.cam.ac.uk, HARPER


On our VAX we have a mailing facility called Gmail, which can be
used for sending mail through different GATEWAYS. You have the
ability to do a CHECK ADDRESS to make sure that the ID@NODE is
correct. So when I run a CHKADD on SEQNET@UK.AC.CAM.PHX I get the
following:
gMail> chkadd seqnet@uk.ac.cam.phx
%gMAIL-E-NOIMPPROT, no implicit protocol defined
for address 'SEQNET@UK.AC.CAM.PHX'
%gMAIL-E-NULLADDR, no valid addresses found.

A friend from CERN said that you may need to REVERSE the order of
the NODE when you are sending messages from EARN to the UK.
So if I REVERSE the order to SEQNET@PHX.CAM.AC.UK and run a
CHKADD then Gmail give the following reply.

gMail> chkadd seqnet@phx.cam.ac.uk
%gMAIL-I-ADDR, gMail address: 'UKACRLGATE%"SEQNET@PHX.CAM.AC.UK"'

This is a valid address from here in Finland and messages sent to
this address get delivered. I hope this is of help to other
EUROPEANS on EARN. JANET most likely is an entirely different
kettle of fish.

Rob "in reverse" Harper

MJB1@VMS-SUPP.CAM.AC.UK (02/06/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 72   ATTIMONELLI%VAXBA0.INFNET 5 Feb 88 BBOARDS on Nucleic Acid colle
From: <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN>  5-FEB-1988 02:29
To: SEQNET
Subject: BBOARDS on Nucleic Acid collections
Date: 5 Feb 88


Via:           UK.AC.RL.EARN; Fri, 05 Feb 88 02:27:26 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 2730; Fri, 05
               Feb 88 02:27:26 GM
Received:
              from IBOINFN.BITNET by UKACRL.BITNET (Mailer X1.25) with BSMTP id
               2728; Fri, 05 Feb 88 02:27:25
Date:          Thu, 4 Feb 88 19:30 N
From:          <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN>
Reply-To:      <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN>
Subject:       BBOARDS on Nucleic Acid collections
To:            MJB1@UK.AC.CAM.VMS-SUPP
X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK"

Message-id: <4495>
Date: THU,  4-FEB-88 19:29 N
From: <ATTIMONELLI@VAXBA0.INFNET>
Reply-To: <ATTIMONELLI%VAXBA0.INFNET@IBOINFN.BITNET>  (alternate reply)
Subject: BBOARDS on Nucleic Acid collections
To:   <MJB1@VMS-SUPP.CAM.AC.UK>
X-Original-To:  MJB1@VMS-SUPP.CAM.AC.UK, ATTIMONELLI


           To the managers of GenBank and EMBL collections and to
           all the Databank users.

This is a note on the release 54 of GenBank that we have recently examined.
In this release the GenBank has changed the FEATURE table format and has
announced that they are moving toward a common format together with the
EMBL and the DNA Japan databank.
We are glad to note that there is at least an intent of reaching a
standardization on the format of the Nucleic Acid Bank, but we want to point
out a few important issues which we hope will be taken into account by both
the scientific community and the Bank managers.

As reported in our paper [ACNUC - a portable retreival system for...(CABIOS,
vol.1(3), 1985, pp.167-172)], we have adopted the GenBank collection for the
generation of the database ACNUC. We preferred the GenBank format to the EMBL
one mainly for the organization of the FEATURE and SITES tables.
In fact we considered very useful the use of SITE keys indicating start and
stop of a region (e.g. -> and  <- ) and boundary between two regions (e.g. /).
Moreover the distinction apported by GenBank between FEATURES table and SITES
table allowed us to easily select the regions that in ACNUC are extracted
as SUBSEQUENCES.
In other words this organization gave us the possibility to extract directly
through ACNUC, specific fragments of a GenBank locus.
This facility is one of the most useful features of ACNUC which makes this
software more flexible and powerful.
The great advantages of the old organization of GenBank has been stressed
also by several researchers (see for example [Nussinov,R. et al. Biochimica et
Biophysica Acta 866 (1986),109-119]).
It is therefore a pity to note that just these useful keys have been abolished.
Moreover in our opinion at the moment the temporary structure of GenBank is
floppy and not very useful.
Of course we do not know the future developments and goals of GenBank but we
would like to stress that with this new format the scientific community has
lost a very important tool.
We wish also to point out several incongruencies encountered between
the news reported in the release notes and the content of the entries files.

In particular in the Primate entry file we have noted :

a) several EMBL sequences have been converted into the GenBank format
   in a pedestrian way (EMBL feature tables have been  simply confined to
   Comments);
b) the feature keys as pept.psi, matp.psi, mRNA.psi, sigp.psi, mRNA+IVS
   are not reported in the Feature keys names (section 3.5.7.1 of the release
   notes);
c) the announced substitution of the key "variation" into the key "variant"
   has not been applied and this has produced an uncorrected tabulation of the
   'from' and 'to/span' fields;

The examples below reported can clarify the situation:

1)             Partial feature table of GenBank entry HUMHBB

    pept.psi  45741    45831     pseudo-hbp, exon 1 [62]
              45953    46175     pseudo-hbp, exon 2 [62]
              47030    47157     pseudo-hbp, exon 3 [62]
    mRNA.psi  45688    47425     pseudo-hbp mRNA [62]
    mRNA+IVS  19289    21098     hbe mRNA (alt.) [19],[40],[52]
    mRNA+IVS  19504    21098     hbe mRNA (alt.) [19],[40],[52]
    mRNA+IVS  19506    21098     hbe mRNA (alt.) [19],[40],[52]
    rpt       66817    66827     Alu flank repeat 5' copy [49],[63]
    rpt       66828    67094     Alu family repeat [49],[63]
    variation  17864    17866     cag in clone lambda-epsilon; g in ph 1.8 [24]
    revision  18641    18646     aatata in [34]; gatgtg in [19]
    refnumbr  19120    19120     numbered 1 in [19]
    refnumbr  19560    19560     numbered 1 in [67]; zero used
    variation  32761    32762     ag in [26]; ga in [25]
    variation  33204    33204     a in [26]; g in [25]
    variation  46596    46597     aa in [62]; a in [63]
    variation  46851    46853     aca in [62]; a in [63]
    variation  47186    47208     ggtccactatgtttgtacctatg in [62]; g in [63]
    variation  47341    47341     t in [62]; tt in [63]
    refnumbr  50768    50768     numbered 1 in [45],[54]

2)    EMBL PTAGGLOG entry converted into GenBank CHPAGGLOG

LOCUS       CHPAGGLOG    1815 bp ds-DNA             pre-entry 12/31/87
DEFINITION  Chimpanzee fetal A-gamma-globin gene.
ACCESSION   X03110
KEYWORDS    A-gamma-globin; direct repeat; gamma-globin; tandem repeat.
SOURCE      chimpanzee (Pan troglodytes).
  ORGANISM  Pan troglodytes
            Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia;
            Eutheria; Primates; Anthropoidea; Hominoidea; Ponginae; Ponginae.
REFERENCE   1  (bases 1 to 1815; enum. 1 to 1815)
  AUTHORS   Slightom,J.L., Chang,L.-Y.E., Koop,B.F. and Goodman,M.
  TITLE     Chimpanzee fetal G-gamma and A-gamma globin gene nucleotide
            sequences provide further evidence of gene conversions in hominine
            evolution
  JOURNAL   Mol Biol Evol 2, 370-389 (1985)
COMMENT     Data kindly reviewed (07-JUL-1986) by Slightom J.L.

               EMBL features not translated to GenBank features:
               key        from     to       description

               PRM          24     28       put. TATA-box
               TRANSCR      55   1647       put. primary transcript
               CAP          55     55       put. cap site
               MSG          55    199       put. exon 1

               IVS         200    321       intron I

               IVS         545   1431       intron iI
               RPT        1123   1162       TG(14) repeat (hot spot sequence
               MSG        1431   1647       put. exon 3

               SITE       1621   1626       put. polyadenylation signal
               POLYA      1647   1647       put. polyadenylation site
FEATURES       from  to/span     description
    pept        108      199     A-gamma-globin (aa 1-31) (199 is 2nd base in
                                 codon)
                322      544     A-gamma-globin (aa 32-105) (322 is 3rd base in
                                 codon)
               1432     1560     A-gamma-globin (aa 106-147)
BASE COUNT      471 a    357 c    474 g    513 t
ORIGIN




We agree that this is an intermediate format, but we believe that it would
have been more correct to distribute the collection in the old format before
completing the conversion.

We cannot utilize the release 54 for updating our database ACNUC.

Since fortunately we have included into our package MERGE (in press on NAR
special issue - Jan 1988) the program TRANSFORM  which convert EMBL format into
the "old" GenBank format, we prefer to use at the moment only the EMBL
collection.

We hope that GenBank can accomplish quickly a revision of the data, checking the
collection in all its structural parts.

We would like to stress another important point.
Many italian research units have adopted our database and softwares (ACNUC and
GLORIA) which are distributed through italian network. This demonstrates
the responsability of the Bank management and the importance for the users
(researchers and software developers) to rely on a structure which could
be easily manipulated with automatic procedures. In this contest we can
welcome changes but only if they provide an improvement.

                                            Marcella Attimonelli

                                            BioComputing Unit Manager

                                            Bari (Italy)
>>>>>>>>>>>>>>>>>>>>>>>>>>>
attimonelli@vaxba0.infnet

MJB1@VMS-SUPP.CAM.AC.UK (02/08/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 74  Christian Burks 5 Feb 88 Genbank Changes
To: SEQNET@CAM.PHX
Date: 6 Feb 1988
Subj: GenBank changes


Received: from lanl.gov by NSS.Cs.Ucl.AC.UK   via Satnet with SMTP  id aa00441;
          6 Feb 88 1:34 GMT
Received: by LANL.GOV (5.54/1.14)
 id AA06065; Fri, 5 Feb 88 18:23:21 MST
Received: by intron.lanl.gov (3.2/5.17)
 id AA05754; Fri, 5 Feb 88 18:34:45 MST
Date: Fri, 5 Feb 88 18:34:45 MST
From: cb < (Christian Burks)cb%intron@gov.lanl>
Message-Id: <8802060134.AA05754@intron.lanl.gov>
To: MJB1@uk.ac.cambridge.vax-vms.support
Subject: Re:  SEQNET Bulletin
Cc: cb <cb%intron@gov.lanl>

Marcella Attimonelli:

Thank you very much for your suggestions and corrections...when we made
the SITES -> FEATURES conversion, we tried to be completely systematic,
but you've obviously caught a few examples where we fell short.  We
appreciate your letting us know.

We are working with EMBL to try and eliminate differences between the
data items in their and our databases...in the meantime, we have
adopted the use of the COMMENT field in GenBank for parking
EMBL features we have not been able to automatically translate
into GenBAnk format.  This of course is not the optimal solution,
but it at least avoids the data being lost altogether at times
when we can't devote the resources to translating the entries
by hand.

I am sorry if the disappearance of SITES caught you by surprise...I had
thought that BBN announced this change in release 52 and/or 53; yours
is the first negative feedback we've had (though I do know of others
who've used the SITES, too).

Please let us know if you encounter any further inconsistencies in
the database, and we'll do our best to address them.

       Christian Burks
       Los Alamos National Laboratory

       GenBank

MJB1@VMS-SUPP.CAM.AC.UK (02/09/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 75  doelz@ch.unibas.urz 8 Feb 88 Searching for electron microscopy di
From: doelz@ch.unibas.urz
To: seqnet@uk.ac.cambridge.phoenix
Subject: Searching for electron microscopy digitizer
Date: 8 Feb 88

Received: from Ean.Ean-Relay.AC.UK by Ean-Relay.AC.UK   via EAN  id aa03409;
          8 Feb 88 14:05 GMT
Return-Receipt-To: doelz@urz.unibas.ch

=======================================================================
Who is using a MacIntosh computer to digitize electron micrographs ?
=======================================================================

In the lab of the biophysics department we use an Apple II with a
digitizer tablet in order to measure the dimensions of molecules visualized
on electron micrographs with the rotary shadowing technique. (Mainly simple
length measurements of rod-like structures in the streaming aquisition mode).
Data then are processed in the Apple to yield histograms and various other
statistics displayed graphically as well as in tables.
The Apple II shall now be replaced by a MacIntosh II.

Does anyone use this computer for similar purposes as described above? We are
interested in a digitizing tablet and useful software evaluating statistics
of the digitized data as well as storing the digitized data in suitable
format for further processing.

Adress:                                   Bitnet adress:
Dr. R. Doelz                              doelz@urz.unibas.ch
Biophysics Department
BIOZENTRUM                                Janet adress:
CH-4056 BASEL                             doelz%urz.unibas.ch@ean-relay.ac.uk

MJB1@VMS-SUPP.CAM.AC.UK (02/09/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 76  From:  HARPER@EARN.FINUH  8 Feb 88  BACKLOG'S ON EARN
From: HARPER@EARN.FINUH
To: seqnet@UK.AC.CAM.PHX
Subject: BACKLOG'S ON EARN

Via:           UK.AC.RL.EARN; Mon, 08 Feb 88 16:16:37 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 8966; Mon, 08
               Feb 88 16:16:37 GM
Received:
          from FINUH.BITNET (HARPER) by UKACRL.BITNET (Mailer X1.25) with BSMTP
               id 8964; Mon, 08 Feb 88 16:16:35
X-Original-To: seqnet@phx.cam.ac.uk, HARPER

Date: 8 Feb 88
For those of you who are not aware of the problems with backlogs of
files on EARN perhaps the following few messages will explain why things
are a bit slow at the moment. So if you are waiting for files be patient.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From: AUFFRET@FRMOP11
Date: Fri, 5 Feb 88 10:40:46 GMT

subject : FRMOP22-CEARN overflow

I strongly think that we are now controlling the situation. JES2
PRIORITY AGING has been completely turned off here. The NOREORD
modification on CEARN gives us a real speed of 6.8 kbps on FRMOP22-CEARN.
About 4500 files are still waiting here on CEARN link.
Yesterday, because of an error in tape operations, about 1000 files
have been unloaded twice on the spool and so will be sent twice at
destination. Sorry.
NOTE : long delays should be expected for large files (over 3000 rec.)
       for still several days.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From: Eric Thomas <ERIC@FRECP11>
Date: Fri, 5 Feb 88 13:44 +01.00

To help  the CEARN-FRMOP22  backlog to  clear up, some  crazed greek
user has started ordering  any and all  available INFO-CPM archive files
from FINHUTC. Each of these  files is 20-30 records. About 100-200  have
already  crossed the CEARN-FRMOP22 line,  60 files  are waiting at SEARN
and over  600 atFINHUTC.  I doubt he will ever  have time to read  this,
but nevermind.
I  am afraid  I will  have to put a limit on the number of files a given
user may order a day in the  next release  of LISTSERV.
This  may cause problems  with servers or  NADs who order files from
LISTSERV to store them  on public disks, but something has to   be done
to prevent this kind of things.

  Eric
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subject: duplicate files

From: Bill Rubin <WGRCU@CUNYVM>
Date: Tue, 2 Feb 88 11:36:03 EST

It appears to me that the traffic problems that are occurring in EARN
are  not being communicated to your user community. That is the only reason
that I can think of for my continuing to see several EARN users a day ask
for  hundreds of files from MACSERVE, KERMIT, TRICKLE, etc. To make matters
worse, and I have said this before, your users seem to have a great
lack of patience when it comes to receiving files, and they are very quick
to re-request the same file again if it hasn't shown up within 24
hours.

How about trying a bit of user education to help alleviate your backlogs?

Bill
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%END OF EXTRACT%%%%%%%%%%%%%%%%%%%%%%%%%%

Rob "for user education" Harper

MJB1@VMS-SUPP.CAM.AC.UK (02/10/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 77  David Kristofferson  8 Feb 88  Subscription to BIONET
From: David Kristofferson <Kristofferson@arpa.bionet-20>
To: ROTH <ROTH%bitnet.pasteur@edu.cuny.cunyvm>
Subject: Subscription to BIONET

Date: 8 Feb 88
Received: from bionet-20.arpa by NSS.Cs.Ucl.AC.UK   via Satnet with SMTP
           id aa06906; 8 Feb 88 17:27 GMT
In-Reply-To: Message from "CHARLES ROTH <ROTH%PASTEUR.BITNET@CUNYVM.CUNY.EDU>" o


Charles,

 Your message came through on the BIONET-NEWS bulletin board.
Kathy Berg (kberg@bionet-20.arpa) can send you information on BIONET
accounts.  You have already mastered posting messages to a bulletin
board.  Our list of bboards follows along with the sample address
format.  To receive copies of our messages I am putting you in touch
with Martin Bishop at SEQNET.  Martin relays copies of BIONET
bulletins to European sites.

    Sincerely,

    Dave Kristofferson
    BIONET Resource Manager

    kristofferson@bionet-20.arpa



                        BULLETINS FROM BIONET
                        ---------------------

The following is our list of bboards available for distribution to
sites outside of BIONET.  For example, all of these bboards may be
routed to BITNET addresses.

BBOARD NAME                  TOPIC
-----------                  -----
BIONET-NEWS                  General BIONET announcements
BIO-MATRIX       Applications of computers to biological databases
CONTRIBUTED-SOFTWARE         Information on programs contributed to BIONET
EMBL-DATABANK       Messages to and from the EMBL database staff
EMPLOYMENT                   Job opportunities
GENBANK-BB                   Messages to and from the GenBank database staff
GENE-EXPRESSION              Scientific Interest Group
GENOMIC-ORGANIZATION         Scientific Interest Group
METHODS-AND-REAGENTS         Requests for information and lab reagents
MOLECULAR-EVOLUTION          Scientific Interest Group
ONCOGENES                    Scientific Interest Group
PC-COMMUNICATIONS            Information on communications software
PC-SOFTWARE                  Information on PC-software for scientists
PIR        Messages to and from the PIR database staff
PLANT-MOLECULAR-BIOLOGY      Scientific Interest Group
PROTEIN-ANALYSIS             Scientific Interest Group
RESEARCH-NEWS                Research news of interest to the community
SCIENCE-RESOURCES      Information about funding agencies, etc.
YEAST-GENETICS               Scientific Interest Group


  Sample BBoard posting address format: MOLECULAR-EVOLUTION@BIONET-20.ARPA


The BIONET bulletin boards are also distributed externally, e.g., to
BITNET addresses, through two methods.  First, each is an ARPANET
mailing list.  Second, each is a private USENET newsgroup for the many
Unix sites that participate in USENET.  If you have a local computing
system, BIONET would like to distribute the bulletin boards to you.
Please contact KRISTOFFERSON or LIEBSCHUTZ for more information.
Equivalences of the Unix USENET newsgroup names to the ARPANET mailing
list names follow:

 bionet.general  .....................BIONET-NEWS
 bionet.jobs  ........................EMPLOYMENT
 bionet.molbio.news  .................RESEARCH-NEWS
 bionet.molbio.seqnet  ...............SEQNET
 bionet.molbio.bio-matrix  ...........BIO-MATRIX
 bionet.molbio.methds-reagnts  .......METHODS-AND-REAGANTS
 bionet.molbio.genbank  ..............GENBANK-BB
 bionet.molbio.embldatabank  .........EMBL-DATABANK
 bionet.molbio.pir  ..................PIR
 bionet.molbio.evolution  ............MOLECULAR-EVOLUTION
 bionet.molbio.gene-express  .........GENE-EXPRESSION
 bionet.molbio.gene-org  .............GENOMIC-ORGANIZATION
 bionet.molbio.oncogenes  ............ONCOGENES
 bionet.molbio.plant  ................PLANT-GENETICS
 bionet.molbio.proteins  .............PROTEIN-ANALYSIS
 bionet.molbio.yeast  ................YEAST-GENETICS
 bionet.sci-resources  ...............SCIENCE-RESOURCES
 bionet.software.pc  .................PC-SOFTWARE
 bionet.software.pc.comm  ............PC-COMMUNICATION
 bionet.software.contrib  ............CONTRIBUTED-SOFTWARE
-------

MJB1@VMS-SUPP.CAM.AC.UK (02/11/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 79  SEQNET 11 Feb 88  Access to US online services for the UK Academi
From: SEQNET
Subject: Access to US online services for the UK Academic Community
Date: 11 Feb 88

                  ONLINE ACCESS TO US COMPUTERS
Access to online services in the US is easy for members of the UK Academic
Community via the JANET - IPSS gateway.  An account at the gateway is
necessary and IPSS charges have to be paid.  Contact you local Computing
Service about getting an account.
To access online services from a terminal connected to a PAD on Janet,
first call the IPSS Gateway:

CALL LON.PSS
or
CALL 00004000004096

Then, using your IPSS account identifier and password call the
computer on Telenet:
eg. for BIONET

(XX10,SECRET).NFS-311040801282

Useful numbers:
BIONET                        NFS-311040801282

HGML                          NFS-31102030002100/GENES
Human Gene Mapping Library at Yale

MSDN                          NFS-311030100342
Microbial Strain Data Network


OMIM                          NFS-311030155030
Online Mendelian Inheritance in Man
by Victor McKusick
at the William H. Welch Medical Library
John Hopkins

I have had no trouble getting to the above.
Please send me further numbers for services of interest to molecular
biologists.

MJB1@VMS-SUPP.CAM.AC.UK (02/13/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 81  ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN 12 Feb 88 DNA Sequence Ana
From: <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN> 12-FEB-1988 18:45
To: MJB1
Subject: DNA Sequence Analysis software


Date: 12 Feb 88
Via:           UK.AC.RL.EARN; Fri, 12 Feb 88 18:44:01 GMT
Received:
          from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 9579; Fri, 12
               Feb 88 18:44:00 GM
Received:
              from IBOINFN.BITNET by UKACRL.BITNET (Mailer X1.25) with BSMTP id
               9577; Fri, 12 Feb 88 18:44:00
Date:          Fri, 12 Feb 88 18:35 N
From:          <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN>
Reply-To:      <ATTIMONELLI%VAXBA0.INFNET@EARN.IBOINFN>
Subject:       DNA Sequence Analysis software
To:            MJB1@UK.AC.CAM.VMS-SUPP
X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK"

Message-id: <4998>
Date: FRI, 12-FEB-88 18:34 N
From: <ATTIMONELLI@VAXBA0.INFNET>
Reply-To: <ATTIMONELLI%VAXBA0.INFNET@IBOINFN.BITNET>  (alternate reply)
Subject: DNA Sequence Analysis software
To:   <MJB1@VMS-SUPP.CAM.AC.UK>
X-Original-To:  mjb1@vms-supp.cam.ac.uk, ATTIMONELLI




       The Molecular Biology groups of Bari use the ACNUC  and  GLORIA
       packages  designed  by the Biocomputing Group of the Department
       of Biochemestry and Molecular Biology of the University of Bari
       (Italy) (M.Attimonelli, C.  Lanave, S.  Liuni, G.Pesole).

       GLORIA package is devoted to the analysis of nucleic  acid  and
       protein sequences.
       This  software  is  user  friendly,  highly  transportable  and
       structured in modular mode.
       Although the  GLORIA  programme,  written  in  Fortran  77,  is
       presently in use on a VAX-Cluster with VMS operating system, it
       may be run on any 32bit-machine whith any operating system  and
       with a FORTRAN-standard compiler.
       GLORIA is highly  modular  structured.   This  physical  scheme
       allows anyone to insert new modules according simple rules.
       Graphic display of several results may be obtained through  the
       non standard GRAPHIC software working with Tektronix devices.
       The analysis becomes very effective when GLORIA works toghether
       with   the   ACNUC  database  (CABIOS  1985  1(3),  pp.167-172)
       containing EMBL and/or GenBank collections.  In addition it can
       be  used  to  analyze  aminoacid sequences from NBRF collection
       restructured in the ACNUC format.
       GLORIA  adds  to  the  algorithms  normally  included  in   the
       available analysis packages those regarding Molecular Evolution
       field.

       Both Gloria and ACNUC packages are available without costs  for
       University and non-profit organizations.

                                             Dr.  Marcella Attimonelli

       ---ATTIMONELLI@VAXBA0.INFNET
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MJB1@VMS-SUPP.CAM.AC.UK (02/17/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 82  MURPHY@UK.AC.AFRC.IPSC  15 Feb 1988  Jobs in Molecular Biology
From: MURPHY@UK.AC.AFRC.IPSC
To: SEQNET@UK.AC.CAM.PHX

Subject: Jobs in Molecular Biology
Date: 15 Feb 1988
=========================

Two  permanent posts are being established in the Institute of Plant Science
Research, Cambridge Laboratory, UK, for DNA sequencers. The successful
appointees will be expected to provide an efficient sequencing service to the
Institute and to assist individual scientists in an advisory capacity to do
their own sequencing. Considerable financial resources will be available to
ensure that advanced techniques and automation of sequencing can be introduced
as they become available. The sequencers would be expected to participate
fully in individual projects and to receive due recognition for their efforts
in any publications resulting from their work.
Although the appointments are to be made initially in Cambridge, the
laboratory is due to move to Norwich in about 1990 to a new building next to
the John Innes Institute. This buiding will contain a room specifically
designed for the DNA sequencing facility.
We are looking for:

1. Higher Scientific Officer
 To manage the sequencing service, including the carrying out of sequencing,
the introduction of new methods, computer analysis of sequencing data and
liason with the scientists for whom the sequencing is being carried out.
 Qualifications: A degree in Biochemistry, Molecular Biology or other relevant
discipline and at least three years postgraduate experience, which must
include experience in DNA sequencing.

2. Scientific Officer
 To carry out sequencing routinely and to maintain equipment in the sequencing
laboratory.
 Qualifications: A degree in Biochemistry, Molecular Biology or other relevant
discipline. Previous experience in DNA sequencing will not be required.

As both posts are permanent and because the service will be of such
importance, we are anxious to ensure that the appointees are well suited to
the work. We would therefore be prepared to hold the positions open for
appropriate candidates if they were unable to take up the appointments
immediately. For further information please contact George Murphy at:
 MURPHY@UK.AC.AFRC.IPSC
 or by telephone: (0223) 840932
 or by post: IPSR Cambridge Laboratory,
             Maris Lane,
      Trumpington,
             Cambridge CB2 2LQ,
       England

I would be very grateful if this message could be brought to the attention of
suitable candidates.

MJB1@VMS-SUPP.CAM.AC.UK (02/18/88)

From: MJB1@VMS-SUPP.CAM.AC.UK

Bulletin_# 83  <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>  17-FEB-1988 15:21  GenB
From: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Date: 17-FEB-1988 15:21
To: SEQNET
Subject: GenBank changes


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Subject:       GenBank changes
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Date: WED, 17-FEB-88 13:31 N
From: <ATTIMONELLI@VAXBA1.INFNET>
Reply-To: <ATTIMONELLI%VAXBA1.INFNET@IBOINFN.BITNET>  (alternate reply)
Subject: GenBank changes
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X-Original-To:  mjb1@vms-supp.cam.ac.uk, ATTIMONELLI


Christian Burks:

we refer to our previous communication about GenBank changes and your answer
dated 6-Feb-1988.
We still believe that it is very important to have the collections structured
in such a way to maintain the maximum information in a machine readable form
allowing a selective retrieval.
You stated in your message that since you "are not able to automatically
translate" EMBL features into GenBank format "you decided to adopt" the
use of COMMENT field for parking EMBL feature.
This, together with the lost of the SITES field, is in our opinion a great
devaluation of the GenBank collection and in particular makes the GenBank
unusable for our software ACNUC.

We have the software TRANSFORM which automatically convert in all its part
the EMBL collection into the "old" GenBank format.
An example is reported below refering to the EMBL entry PTAGGLOG already
mentioned in our previous message.

If you are interested in the software TRANSFORM please contact us at your
earlier convenience.

                                         Dr. Marcella Attimonelli


>>>>>>>>>>

EMBL PTAGGLOG entry converted into GenBank format by TRANSFORM program


LOCUS       PTAGGLOG     1815 bp    DNA             entered   02/16/87
DEFINITION  Chimpanzee fetal A-gamma-globin gene
ACCESSION   X03110
KEYWORDS    gamma-globin; A-gamma-globin; direct repeat; tandem repeat.
SOURCE
  ORGANISM  Pan troglodytes ;(chimpanzee, chimpanze, Chimpanse)
            Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia;
            Eutheria; Primates.
REFERENCE   1  (bases 1 to 1815)
  AUTHORS   Slightom,J.L., Chang,L.-Y.E., Koop,B.F. and Goodman,M.
  TITLE     Chimpanzee fetal G-gamma and A-gamma globin gene nucleotide
            sequences provide further evidence of gene conversions in hominine
            evolution
  JOURNAL   Mol. Biol. Evol. 2, 370-389 (1985)
COMMENT     History:
            17-JAN-1986  (annotation)
            Data kindly reviewed (07-JUL-1986) by Slightom J.L.
FEATURES       from  to/span     description
    pept         55      199     put. exon 1
    matp        108      199     A-gamma-globin (aa 1-31)
                                 (199 is 2nd base in codon)
                322      544     A-gamma-globin (aa 32-105)
                                 (322 is 3rd base in codon)
               1432     1557     A-gamma-globin (aa 106-147)
    pept       1431     1647     put. exon 3
    RNA          55     1647     put. primary transcript
  SITES
    ->prm        24        1     put. TATA-box start
    prm<-        28        1     put. TATA-box end
    cap          55        0     put. cap site
    ->pept       55        1     put. exon 1 start
    ->RNA        55        1     put. primary transcript start
    ->matp      108        1     A-gamma-globin (aa 1-31)
                                 (199 is 2nd base in codon) start
    matp/ivs    199        0     A-gamma-globin (aa 1-31)
                                 (199 is 2nd base in codon) end/intron
                                 start
    pept<-      199        1     put. exon 1 end
    ivs/matp    322        0     intron end /A-gamma-globin (aa 32-105)
                                 (322 is 3rd base in codon) start
    matp/ivs    544        0     A-gamma-globin (aa 32-105)
                                 (322 is 3rd base in codon) end/intron
                                 start
    ->rpt      1123        1     TG(14) repeat (hot spot sequence start
    rpt<-      1162        1     TG(14) repeat (hot spot sequence end
    ->pept     1431        1     put. exon 3 start
    ivs/matp   1432        0     intron end /A-gamma-globin (aa 106-147
                                 ) start
    matp<-     1557        1     A-gamma-globin (aa 106-147) end
    ->site     1621        1     put. polyadenylation signal start
    site<-     1626        1     put. polyadenylation signal end
    polya      1647        0     put. polyadenylation site
    pept<-     1647        1     put. exon 3 end
    RNA<-      1647        1     put. primary transcript end
BASE COUNT      471 A    357 C    474 G    513 T
ORIGIN
        1 CCGGCGGCTG GCTAGGGATG AAGAATAAAA GGAAGCACCC TCCAGCAGTT CCACACACTC
       61 GCTTCTGGAA CGTCTGAGGT TATCAATAAG CTCCTAGTCC AGACGCCATG GGTCATTTCA
      121 CAGAGGAGGA CAAGGCTACT ATCACAAGCC TGTGGGGCAA GGTGAATGTG GAAGATGCTG
      181 GAGGAGAAAC CCTGGGAAGG TAGGCTCTGG TGACCAGGAC AAGGGAGGGA AGGAAGGACC
      241 CTGTGCCTGG CAAAAGTCCA GGTCACTTCT CAGGATTTGT GGCACCTTCT GACTGTCAAA
      301 CTGTTCTTGT CAATCTTACA GGCTCCTGGT TGTCTACCCA TGGACCCAGA GGTTCTTTGA
      361 CAGCTTTGGC AACCTGTCCT CTGCCTCTGC CATCATGGGC AACCCCAAGG TCAAGGCACA
      421 TGGCAAGAAG GTGCTGACTT CCTTGGGAGA TGCCATAAAG CACCTGGATG ACCTCAAGGG
      481 CACCTTTGCC CAGCTGAGTG AACTGCACTG TGACAAGCTG CATGTGGATC CTGAGAACTT
      541 CAAGGTGAGT CCAGGAGATG TTTCAGCCCT GTTGCCTTTA GTCTGGAGGC AACTTAGACA
      601 ACTGAGTATT AATCTGAGCA CAGCTGAATC TACCCACAGG GTGTAAACTA TTTGAAGATA
      661 TTGGGGTTGG GAGTGAAGGA ACTGCAGAGG ACTAACTGGG CTGAGACCCA GTGGTAATGT
      721 TTTAGGGCCT AAGGAGTGCC TCTAAAAATC TAGATGGACA ATTTTGACTT TGAGAATAGA
      781 GAGGTGGAAA TGAGGAAAAT GACTTTTCTT TATTAGATTC CAGTAGAAAG AACTTTCATC
      841 TTTCCCTCAT TTTTGTTGTT TTAAAACATC TATCTGGAGG CAGGACAAGT ATGGTCATTA
      901 AAAAGATGCA GGCAGAAGGC ATATATTGGC TCAGTCAAAG TGGGGAACTT TGGTGGCCAA
      961 ACATATATTG CTAAGGCTAT TCCTATGTCA TCTGGACACA TATAAAATGC TGCTAATGCT
     1021 TCATTACAAA CTTATATCCT TTAATTCCAG ATGGGGGCAA AGTATGTCCA GGGGTGAGGA
     1081 ACAATTGGAA CATTTGGGCT GGAGTAGATT TTGAAAGTCA GCTGTGAGTT TGTGTGTGTG
     1141 TGTGTGTGTG TGTGTGTGCG TGTCAGCGTG TGTTTCTTTT AACGTCTTCA GCCTACAACA
     1201 TACAGGGTTC ATGGTGGCAA GAAGATAGCA AGATTTAAAT TATGGCCAGT GACTAGTGCT
     1261 GCAAGGGGAA CAACTACCTG CATTTAATGG GAAGGCAAAA TCTCAGGCTT TGAGGGAAGT
     1321 TAACATAGGC TTGATTCTGG GTGGAAGCTG GGTGTGTAGT TATCTGGAGG CCAGGCTGGA
     1381 GCTCTCAGCT CACTATGGGT TCATCTTTAT TGTCTCCTTT CATCTCAACA GCTCCTGGGA
     1441 AATGTGCTGG TGACCGTTTT GGCAATCCAT TTCGGCAAAG AATTCACCCC TGAGGTGCAG
     1501 GCTTCCTGGC AGAAGATGGT GACTGCAGTG GCCAGTGCCC TGTCCTCCAG ATACCACTGA
     1561 GCCTCTTGCC CATGATTCAG AGCTTTCAAG GATAGGCTTT ATTCTGCAAG CAATACAAAT
     1621 AATAAATCTA TTCTGCTGAG AGATCACACA TGATTTTCTT CAGCTCTTTT TTTTACATCT
     1681 TTTTAAATAC ATGAGCCACA AAGGGTTTAT ATTGAGGGAA GTGTGTATGT GTATTTCTGC
     1741 ATGCCTGTTT GTGTTTGTGG TGTGTGCATG CTCCTCATTT ATTTTTATAT GAGATGTGCA
     1801 TTTTGATGAG CAAAT
//