gribskov@ov ("Gribskov, Michael") (12/17/90)
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@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@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 +------------------------------------------------------------------------------ haywire.nmsu.edu gm (gene modeler) package 128.123.001.032 Chris Fields*, cfields@nmsu.edu ------------------------------------------------------------------------------- mcclb0.med.nyu.edu USENET genbank software Ross Smith, smith@mcclb0.med.nyu.edu +------------------------------------------------------------------------------ ncifcrf.gov Delila sequence analysis system (/pub/delila) (150 programs) 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 192.54.41.20 future access to EMBL server see netserv@embl entry below Rainer Fuchs fuchs@embl.bitnet +------------------------------------------------------------------------------ flat.nig.ac.jp DNA Data Bank of Japan 133.39.128.2 Genbank, EMBL, DDBJ NBRF, Swissprot, GENPEPT Sanzo Miyazawa smiyazaw@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@genbank.bio.net FASTA searches consultant@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@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) many databases,e.g. alu sequences list SwissEnzyme, Prosite GCG (3) format codon tables Reinhard Doelz, Journal tables of contents doelz@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@ncbi.nlm.nih.gov (help and information) (/repository) EPD,LiMB,REBASE,SwissENZYME metabolism, mol-model Transcription factor database (TFD) D. Ghosh*, ghosh@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@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@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 Genbank and GENPEPT 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) SwissProt, Prosite PDB (Brookhaven db) PC, UNIX, Mac & VAX software LiMB, ECD, EPD, TFD, SwissEnzyme DROS, SEQREF 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(updated 2x daily) Sanzo Miyazawa GENPEPT, EMBL(+new entries) smiyazaw@nig.ac.jp SwissProt, PIR, PRF keyword searches by author, journal, accession, and description +------------------------------------------------------------------------------ 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) 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)