My thanks to all those who responded to my request for information about
FTP and servers sites of interest to molecular biologists. The response
was considerably greater than I expected and it therefore took some time
to produce the following list.
I not completely satisfied with this list, but I thought it would be
good to get the current version distributed, and to work on an improved
version next year. I think that a more detailed version of the list
would be useful; I would particularly appreciate some feedback on the
level of detail that people would like to see and suggestions on the
most useful format for a more detailed listing. If you know of other
sites that should be included, or find errors please let me know.
Michael Gribskov
gribskov at ncifcrf.gov
--------------------------------------------------------------------------------
Molecular Biology FTP and Server List (16 December 1990)
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 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.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Specific software packages and smaller FTP sites
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
address contents
responsible person/more information
+-----------------------------------------------------------------------------
evolution.genetics.washington.edu PHYLIP phylogeny package v3.3
128.208.128.1
Joe Felsenstein*, joe at genetics.washington.edu
+-----------------------------------------------------------------------------
anthro.utah.edu. PHYLIP phylogeny package v3.3
128.110.192.93 (officially sanctioned by author)
Alan Rogers, rogers at anthro.utah.edu
+------------------------------------------------------------------------------
haywire.nmsu.edu gm (gene modeler) package
128.123.001.032
Chris Fields*, cfields at nmsu.edu
-------------------------------------------------------------------------------
mcclb0.med.nyu.edu USENET genbank software
Ross Smith, smith at mcclb0.med.nyu.edu
+------------------------------------------------------------------------------
ncifcrf.gov Delila sequence analysis system
(/pub/delila) (150 programs)
Tom Schneider*, toms at ncifcrf.gov
+------------------------------------------------------------------------------
uvaarpa.virginia.edu FASTA database search
(/public_access/fasta.shar) program
William Pearson*, wrp at virginia.edu
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Larger FTP sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
embl-heidelberg.de EMBL
192.54.41.20 future access to EMBL server
see netserv at embl entry below
Rainer Fuchs
fuchs at embl.bitnet
+------------------------------------------------------------------------------
flat.nig.ac.jp DNA Data Bank of Japan
133.39.128.2 Genbank, EMBL, DDBJ
NBRF, Swissprot, GENPEPT
Sanzo Miyazawa
smiyazaw at nig.ac.jp
+------------------------------------------------------------------------------
genbank.bio.net Genbank
134.172.1.160 Genbank database (quarterly)
(/Public) Genbank updates (weekly & nightly)
GenPept db & updates
Dave Kristofferson, EMBL db & updates
kristoff at genbank.bio.net FASTA searches
consultant at genbank.bio.net On-line services
software
-------------------------------------------------------------------------------
iubio.bio.indiana.edu IUBIO archive
129.79.1.101 Mac,VAX,Atari,DOS software
LiMB,EPD,TFD,REBASE,DROS
Don Gilbert, Prosite
gilbertd at 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 at 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 at 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) many databases,e.g.
alu sequences list
SwissEnzyme, Prosite
GCG (3) format codon tables
Reinhard Doelz, Journal tables of contents
doelz at urz.unibas.ch LiMB,TFD,ECD,EPD,REBASE,DROS
+------------------------------------------------------------------------------
ncbi.nlm.nih.gov Natl. Center for Biotech. Information
130.14.20.1 NCBI software
Geninfo db documentation
Scott Federhen,
federhen at ncbi.nlm.nih.gov (help and information)
(/repository) EPD,LiMB,REBASE,SwissENZYME
metabolism, mol-model
Transcription factor database (TFD)
D. Ghosh*, ghosh at ncbi.nlm.nih.gov
(/toolbox) assorted public domain software
(/pub) more software - blast, fasta, macaw,etc
(/pub/aimb-db) AI and molecular biology researchers db
Lawrence Hunter*, hunter at nlm.nih.gov
+------------------------------------------------------------------------------
nic.funet.fi Finnish State Supercomputer Center
128.214.6.100 Center for Scientific Computing
(pub/misc/molbio) VAX, Unix, DOS, Mac software
many non-biological applications
Rob Harper, harper at csc.fi
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Server sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
bioserve%genome at lanl.gov (2) Los Alamos National Laboratory server
Genbank documentation
Michael Cinofsky, software archive (future)
michael%domain at lanl.gov
-------------------------------------------------------------------------------
fileserv at gunbrf.bitnet (2) PIR server
Genbank and GENPEPT
Dr. John S. Garavelli, garavell at gunbrf.bitnet
Ms. Kathryn Sidman, pirmail at gunbrf.bitnet
+------------------------------------------------------------------------------
gene-server at bchs.uh.edu (1) U Houston gene server
Genbank sequence db
gene-server-management at bchs.uh.edu PIR sequence db
UNIX,DOS,VMS,Mac software
Cray software (future)
BioMatrix archive
Molecular evolution bb archive
FASTA searches
-------------------------------------------------------------------------------
listserv at 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 at csc.fi (Newsgroup at irlearn.bitnet)
e.g. AGEING at irlearn.bitnet
-------------------------------------------------------------------------------
listserv at taunivm.bitnet (2) photosynthesis researchers bb
(photosyn at taunivm.bitnet)
Jonathan Marder, marder at hujiagri.bitnet
-------------------------------------------------------------------------------
listserv at utoronto.bitnet (2) U Toronto list server
John Cargill GCG (3) software discussion group
cargill at utoroci.bitnet (info-gcg at utoronto.bitnet)
cargill at galen.oci.utoronto.ca
+------------------------------------------------------------------------------
netserv at embl.bitnet (2) EMBL server
EMBL (updated daily)
SwissProt, Prosite
PDB (Brookhaven db)
PC, UNIX, Mac & VAX software
LiMB, ECD, EPD, TFD, SwissEnzyme
DROS, SEQREF
search at embl.bitnet (2) FASTA searches
quick at embl.bitnet (2) Quicksearch (4) searches
Rainer Fuchs, fuchs at embl.bitnet
-------------------------------------------------------------------------------
netserv at flat.nig.ac.jp (2) FLAT DB E-Mail Network Server
DDBJ,Genbank(updated 2x daily)
Sanzo Miyazawa GENPEPT, EMBL(+new entries)
smiyazaw at nig.ac.jp SwissProt, PIR, PRF
keyword searches by author,
journal, accession, and description
+------------------------------------------------------------------------------
Genbank server
search at genbank.bio.net (2) FASTA searches
retrieve at genbank.bio.net Sequence retrieval
genbank at genbank.bio.netconsultant at genbank.bio.net (help with FASTA)
retrieve-request at genbank.bio.net (help with retrieval)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Anticipated availability: fall of 1991.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Kenneth Kidd, Martin Mador Biology Software Info. Clearinghouse
genmlm at 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)
DROS Drosophila clones, maps and genetic deficiencies databases
ECD E. coli database
EMBL European Molecular Biology Laboratory DNA sequence db
EPD Eukaryotic Promoter Database (Philip Bucher)
GENPEPT Genbank translated protein database
LiMB Listing of Molecular Biology databases (Lawerence Hunter,NCBI)
PIR Protein Information Resource (NBRF protein sequence db)
PRF Protein Research Foundation db
REBASE Restriction Enzyme database (Richard Roberts)
SEQREF SEQANALREF - sequence analysis reference list
TFD Transcription Factor Database (D.Ghosh,NCBI)
