gribskov@FCRFV1.NCIFCRF.GOV ("Gribskov, Michael") (03/12/91)
Archive-name: bionet/molbio/molbio-ftp-list/1991-03-07
Original-posting-by: gribskov@FCRFV1.NCIFCRF.GOV ("Gribskov, Michael")
Original-subject: ftp sites, Re: DOS software
Reposted-by: emv@ox.com (Edward Vielmetti)
This is an updated version of the list I previously posted to bionews.
I did not cross post it to bio-software because I thought there would be
a heavy overlap. However, in response to the recent questions about
DOS software, here is the most recent version. In addition to sites
mentioned in other postings, I note that there is one other listing that
meentions DOS, the NIC.FUNET site in Finland. I hope this is helpful.
* * * * * * * * * * * * * *
* * * * * * * * * * * * * *
Molecular Biology FTP and Server List
7 March 1991
Michael Gribskov
gribskov@ncifcrf.gov
IF YOU REDISTRIBUTE THIS LIST, PLEASE PRESERVE THIS HEADER
-------------------------------------------------------------------------------
The address for each site is shown in the left column, with the numerical
intenet address below, if it was available. This is followed by the mail
address of the responsible person, or an address for more information. For
FTP sites, the directory containing the relevent material is shown in
parentheses if it is other than the default directory. Note that the larger
FTP sites may have a great deal of material of general interest in addition
to what is shown here.
For bulletin boards, the subscription address is shown in the left
column, and the address for actual message in parentheses in the center
column.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Software packages, databases, and smaller FTP sites
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
address contents
responsible person/more information
+-----------------------------------------------------------------------------
evolution.genetics.washington.edu PHYLIP phylogeny package v3.3
128.95.12.41
Joe Felsenstein*, joe@genetics.washington.edu
+-----------------------------------------------------------------------------
anthro.utah.edu. PHYLIP phylogeny package v3.3
128.110.192.93 (officially sanctioned by author)
Alan Rogers, rogers@anthro.utah.edu
+------------------------------------------------------------------------------
frodo.mgh.harvard.edu Codon usage tables for all major species
132.183.190.10
( [.codon] )
Mike Cherry*, cherry@frodo.mgh.harvard.edu
+------------------------------------------------------------------------------
haywire.nmsu.edu gm (gene modeler) package
128.123.001.032
Chris Fields*, cfields@nmsu.edu
+------------------------------------------------------------------------------
lhc.nlm.nih.gov AIMB (AI and mol.bio.
130.14.1.128 researchers database)
(/pub/aimb-db)
Lawrence Hunter*, hunter@nlm.nih.gov
-------------------------------------------------------------------------------
mcclb0.med.nyu.edu USENET genbank software
Ross Smith, smith@mcclb0.med.nyu.edu
+------------------------------------------------------------------------------
ncifcrf.gov Delila sequence analysis system
129.43.1.11 (150 programs)
(/pub/delila)
Tom Schneider*, toms@ncifcrf.gov
+------------------------------------------------------------------------------
uvaarpa.virginia.edu FASTA database search
(/public_access/fasta.shar) program
William Pearson*, wrp@virginia.edu
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Larger FTP sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
embl-heidelberg.de EMBL server
192.54.41.20 EMBL (updated daily)
SWISS-PROT (and updates), PDB
DROMAP, ECD, ENZYME, EPD, LiMB, NGDD,
Rainer Fuchs PROSITE, SEQANALREF, TFD.
fuchs@embl.bitnet PC, UNIX, Mac & VAX software
+------------------------------------------------------------------------------
flat.nig.ac.jp
133.39.128.2 GenBank, EMBL, DDBJ, PIR, SWISS-PROT,
GENPEPT, LiMB
Software: FLAT DB search/retrieval
program for UNIX
Sanzo Miyazawa
smiyazaw@flat.nig.ac.jp
+------------------------------------------------------------------------------
genbank.bio.net Genbank server
134.172.1.160 Genbank db (quarterly)
(/Public) Genbank updates (weekly & nightly)
GENPEPT db & updates
EMBL db & updates
SWISS-PROT db (soon available)
ALU, ENZYME, PROSITE, REBASE,
Dave Kristofferson, SEQANALREF.
kristoff@genbank.bio.net software
consultant@genbank.bio.net On-line services
+------------------------------------------------------------------------------
iubio.bio.indiana.edu IUBIO archive
129.79.1.101 Mac,VAX,Atari,DOS software
DROMAP, EPD, LiMB, PROSITE, REBASE,
Don Gilbert, TFD
gilbertd@iubio.bio.indiana.edu Phylip
Authorin program
-------------------------------------------------------------------------------
mbcrr.harvard.edu Molecular Biology Computer
134.174.51.4 Research Resource
software
Temple Smith, PLSEARCH pattern db
tsmith@mbcrr.harvard.edu MASE 3.1 multiple sequence editor
+------------------------------------------------------------------------------
menudo.uh.edu U Houston archive
129.7.1.6 Genbank sequence db
PIR sequence db
Dan Davison, UNIX,DOS,VMS,Mac software
dbd@theory.bchs.uh.edu Cray software (future)
BioMatrix archive
Molecular evolution bb archive
+------------------------------------------------------------------------------
modl.unibas.ch Biocomputing server
131.152.1.2 Biozentrum, Universitaet Basel
(/biology/EMBnet) EMBL ( updated daily)
(/biology/databases) ALU, DROMAP, ECD, ENZYME, EPD, LiMB,
NGDD, PROSITE, REBASE, SEQANALREF,
TFD.
GCG (3) format codon usage tables
Reinhard Doelz, BIOSCI Journal tables of contents
doelz@urz.unibas.ch Amos Bairoch*, bairoch@cgecmu51.bitnet
+------------------------------------------------------------------------------
ncbi.nlm.nih.gov Natl. Center for Biotech. Information
130.14.20.1 NCBI software
Geninfo db documentation
Scott Federhen,
federhen@ncbi.nlm.nih.gov (help and information)
(/repository) ENZYME, EPD, LiMB, NGDD, PROSITE,
REBASE, SEQANALREF, TFD
metabolism, mol-model
(/toolbox) assorted public domain software
(/pub) more software - BLAST, FASTA, MACAW, etc
(/pub/aimb-db) AIMB db
Lawrence Hunter*, hunter@nlm.nih.gov
+------------------------------------------------------------------------------
nic.funet.fi Finnish State Supercomputer Center
128.214.6.100 Center for Scientific Computing
(pub/sci/molbio) VAX, Unix, DOS, Mac software
many non-biological applications
Rob Harper, harper@csc.fi
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Server sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
bioserve%genome@lanl.gov (2) Los Alamos National Laboratory server
Genbank documentation
Michael Cinofsky, software archive (future)
michael%domain@lanl.gov
-------------------------------------------------------------------------------
fileserv@gunbrf.bitnet (2) PIR server
PIR, NBRF Nucleic, Genbank, EMBL
Dr. John S. Garavelli, garavell@gunbrf.bitnet
Ms. Kathryn Sidman, pirmail@gunbrf.bitnet
+------------------------------------------------------------------------------
gene-server@bchs.uh.edu (1) U Houston gene server
Genbank sequence db
gene-server-management@bchs.uh.edu PIR sequence db
UNIX,DOS,VMS,Mac software
Cray software (future)
BioMatrix archive
Molecular evolution bb archive
FASTA searches
-------------------------------------------------------------------------------
listserv@irlearn.bitnet (2) IRLEARN list server
BIOSCI newsgroups & archives
Newsgroups:
AGEING, AG-FORST, BIO-NAUT, BIONEWS,
BIO-JRNL, BIOMATRX, BIO-SOFT, CHROM-22,
EMBL-DB, BIOJOBS, GENBANKB, GENE-ORG,
ORG, GNOME-PR, METHODS, MOL-EVOL,
POP-BIO, PROTEINS, SCI-RES
Rob Harper, harper@csc.fi (Newsgroup@irlearn.bitnet)
e.g. AGEING@irlearn.bitnet
+------------------------------------------------------------------------------
listserv@taunivm.bitnet (2) photosynthesis researchers bb
(photosyn@taunivm.bitnet)
Jonathan Marder, marder@hujiagri.bitnet
+------------------------------------------------------------------------------
listserv@utoronto.bitnet (2) U Toronto list server
John Cargill GCG (3) software discussion group
cargill@utoroci.bitnet (info-gcg@utoronto.bitnet)
cargill@galen.oci.utoronto.ca
+------------------------------------------------------------------------------
netserv@embl.bitnet (2) EMBL server
EMBL (updated daily)
SWISS-PROT (and updates), PDB
DROMAP, ECD, ENZYME, EPD, LiMB, NGDD,
PROSITE, SEQANALREF, TFD.
PC, UNIX, Mac & VAX software
search@embl.bitnet (2) FASTA searches
quick@embl.bitnet (2) Quicksearch (4) searches
Rainer Fuchs, fuchs@embl.bitnet
+------------------------------------------------------------------------------
netserv@flat.nig.ac.jp (2) FLAT DB E-Mail Network Server
DDBJ,Genbank,EMBL (updated 2x daily)
GENPEPT, SWISS-PROT, PIR, PRF
Sanzo Miyazawa keyword searches by author,
smiyazaw@flat.nig.ac.jp journal, accession, and description
+------------------------------------------------------------------------------
pythia@cis.ucsc.edu (2) Alu sequence identification server
Aleksandar Milosavljevic
pythia-admin@cis.ucsc.edu
milosav@cis.ucsc.edu
+------------------------------------------------------------------------------
Genbank server
search@genbank.bio.net (2) FASTA searches
retrieve@genbank.bio.net Sequence retrieval
genbank@genbank.bio.net
consultant@genbank.bio.net (help with FASTA)
retrieve-request@genbank.bio.net (help with retrieval)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Anticipated availability: fall of 1991.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Kenneth Kidd, Martin Mador Biology Software Info. Clearinghouse
genmlm@yalevm.bitnet Online software database
peer reviews
software archive
bug reports
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
* indicates that the contact person is the author of the database or program
(1) for information on this server send the message "help" in subject
(2) for information on this server send the message "help" as the first line of
the message
(3) Genetics Computer Group Sequence Analysis Package
(4) The GCG (3) program quicksearch with enhancements added at EMBL is
used to check if a new sequence has been previously sequenced. The
search is much faster than FASTA, but is will only find nearly identical
sequences.
db = database
bb = bulletin board (or discussion group)
Sequence data banks
DDBJ DNA Data Bank of Japan db
EMBL European Molecular Biology Laboratory DNA sequence db
GENBANK GenBank nucleic acid db
GENPEPT GenBank translated protein db
PIR Protein Information Resource (NBRF protein sequence db)
SWISS-PROT SWISS-PROT protein sequence db
Other data banks
AIMB AI and molecular biology researchers db (Hunter, NLM)
ALU Alu Sequence db (Jurka)
DROMAP Drosophila Genetic Maps db (M. Ashburner, Cambridge)
ECD Escherichia coli db (M. Kroeger, Giessen)
ENZYME Enzymes nomenclature db (A. Bairoch, Geneva)
EPD Eukaryotic Promoter db (P. Bucher, Stanford)
LiMB Listing of Molecular Biology databases (C. Burks, Los Alamos)
NGDD Normalized gene maps for E.coli, S.typh., etc. (Y. Abel, Montreal)
PDB Protein Data Bank (3D structures) (E. Abola, Brookhaven)
PROSITE Dictionary of Protein Sites and Patterns (A. Bairoch, Geneva)
PRF Protein Research Foundation db
REBASE Type 2 Restriction Enzymes db (R. Roberts, CSH)
SEQANALREF Sequence analysis reference list (Bairoch, Geneva)
TFD Transcription Factors Relational db (D. Ghosh, NCBI)