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
Received: from EMBL(CAMERON) by UKACRL (Mailer X1.25) id 3770;
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, 1968daemon@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 GroupMJB1@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.phxMJB1@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" HarperMJB1@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
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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.infnetMJB1@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
GenBankMJB1@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.ukMJB1@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
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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" HarperMJB1@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
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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
---EARN%IBOINFN::ATTIMONELLI%VAXBA0.INFNET FOR EARNETMJB1@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
Via: UK.AC.RL.EARN; Wed, 17 Feb 88 15:20:28 GMT
Received:
from UKACRL by UK.AC.RL.IB (Mailer X1.25) with BSMTP id 0023; Wed, 17
Feb 88 15:20:28 GM
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0001; Wed, 17 Feb 88 15:20:26
Date: Wed, 17 Feb 88 13:31 N
From: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Reply-To: <ATTIMONELLI%VAXBA1.INFNET@EARN.IBOINFN>
Subject: GenBank changes
To: MJB1@UK.AC.CAM.VMS-SUPP
X-Original-To: "MJB1@VMS-SUPP.CAM.AC.UK"
Message-id: <6589>
Date: WED, 17-FEB-88 13:31 N
From: <ATTIMONELLI@VAXBA1.INFNET>
Reply-To: <ATTIMONELLI%VAXBA1.INFNET@IBOINFN.BITNET> (alternate reply)
Subject: GenBank changes
To: <MJB1@VMS-SUPP.CAM.AC.UK>
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
//