-------------------------------------------------------------------------------- Molecular Biology FTP and Server List Produced by: Michael Gribskov / gribskov@ncifcrf.gov Release of 16 December 1990 Extensively modified by Amos Bairoch: 18 December 1990 -------------------------------------------------------------------------------- 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 : evolution.genetics.washington.edu (128.208.128.1) Contents: PHYLIP phylogeny package v3.3 Contact : Joe Felsenstein [*] joe@genetics.washington.edu ------------------------------------------------------------------------------ Address : anthro.utah.edu (128.110.192.93) Contents: PHYLIP phylogeny package v3.3 (officially sanctioned by author) Contact : Alan Rogers rogers@anthro.utah.edu ------------------------------------------------------------------------------ Address : haywire.nmsu.edu (128.123.001.032) Contents: gm (gene modeler) package Contact : Chris Fields [*] cfields@nmsu.edu ------------------------------------------------------------------------------ Address : mcclb0.med.nyu.edu Contents: USENET GenBank software Contact : Ross Smith smith@mcclb0.med.nyu.edu ------------------------------------------------------------------------------- Address : ncifcrf.gov Contents: Delila sequence analysis system (150 programs) In: /pub/delila Contact : Tom Schneider [*] toms@ncifcrf.gov ------------------------------------------------------------------------------ Address : uvaarpa.virginia.edu Contents: FASTA database search program In: /public_access/fasta.shar Contact : William Pearson [*] wrp@virginia.edu ------------------------------------------------------------------------------ [*] Indicates that the contact person is the author of the database or program +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Larger FTP sites +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------------------------------- Organism: EMBL Address : embl-heidelberg.de (192.54.41.20) Contents: Future access to EMBL server (see netserv@embl entry below) Contact : Rainer Fuchs fuchs@embl.bitnet ------------------------------------------------------------------------------- Organism: DNA Data Bank of Japan Address : flat.nig.ac.jp (133.39.128.2) Contents: GenBank, GenPept, EMBL, DDBJ, NBRF, SWISS-PROT. Contact : Sanzo Miyazawa smiyazaw@nig.ac.jp +------------------------------------------------------------------------------ Organism: GenBank On-line Service (GOS) Address : genbank.bio.net (134.172.1.160) Contents: GenBank (+ weekly and nightly updates), GenPept SWISS-PROT (future) ALU, ENZYME, PROSITE, REBASE, SEQANALREF (In subdirectories of /pub/db) FASTA searches On-line services Various Mac, VAX, DOS software Contact: Dave Kristofferson kristoff@genbank.bio.net or consultant@genbank.bio.net ------------------------------------------------------------------------------- Organism: IUBIO archive Address : iubio.bio.indiana.edu (129.79.1.101) Content : Various Mac, VAX, Atari, DOS software Authorin data entry program PHYLIP phylogeny package AIMB, DROMAP, EPD, LiMB, PROSITE, REBASE, TFD Contact : Don Gilbert gilbertd@iubio.bio.indiana.edu ------------------------------------------------------------------------------- Organism: Molecular Biology Computer Research Resource Address : mbcrr.harvard.edu (134.174.51.4) Contents: PLSEARCH pattern db and software MASE 3.1 multiple sequence editor Contact : Temple Smith tsmith@mbcrr.harvard.edu ------------------------------------------------------------------------------- Organism: University of Houston archive Address : menudo.uh.edu (129.7.1.6) Contents: GenBank, PIR Various Mac, VAX, Atari, DOS software Cray software (future) BioMatrix archive Molecular evolution bb archive Contact : Dan Davison dbd@theory.bchs.uh.edu ------------------------------------------------------------------------------- Organism: Basel Biozentrum Biocomputing server (EMBnet SWISS node) Address : modl.unibas.ch (131.152.1.2) Contents: EMBL (+ daily updates) (In /biology/EMBnet) ALU, DROMAP, ECD, ENZYME, EPD, LiMB, NGDD, PROSITE, REBASE, SEQANALREF, TFD. GCG (3) format codon tables BIOSCI Journals tables of contents (In subdirectories of /biology/databases) Contact : Reinhard Doelz doelz@urz.unibas.ch Amos Bairoch bairoch@cgecmu51.bitnet ------------------------------------------------------------------------------- Organism: National Center for Biotechnology Information (NCBI) Address : ncbi.nlm.nih.gov (130.14.20.1) Contents: NCBI software: blast, fasta, macaw, etc. (In /pub) Geninfo db documentation Assorted Geninfo software (In /toolbox) AIMB, ENZYME, EPD, LiMB, NGDD, PROSITE, REBASE, SEQANALREF, TFD, metabolism, mol-model (In subdirectories of /repository or in /pub/aimb-db) Contact : Scott Federhen federhen@ncbi.nlm.nih.gov ------------------------------------------------------------------------------- Organism: Finnish State Supercomputer Center / Center for Scientific Computing Address : nic.funet.fi (128.214.6.100) VAX, Unix, DOS, Mac software (In /pub/misc/molbio) Many non-biological applications Contact : Rob Harper harper@csc.fi ------------------------------------------------------------------------------- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Server sites +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Organism: Los Alamos National Laboratory server Address : bioserve%genome@lanl.gov (2) Contents: GenBank documentation Software archive (future) Contact : Michael Cinofsky michael%domain@lanl.gov ------------------------------------------------------------------------------- Organism: PIR server Address : fileserv@gunbrf.bitnet (2) Contents: PIR Software services Contact : John S. Garavelli garavell@gunbrf.bitnet Kathryn Sidman pirmail@gunbrf.bitnet ------------------------------------------------------------------------------ Organism: University of Houston gene server Address : gene-server@bchs.uh.edu (1) Contents: GenBank, PIR Various Mac, VAX, Atari, DOS software Cray software (future) BioMatrix archive Molecular evolution bb archive FASTA searches Contact : gene-server-management@bchs.uh.edu ------------------------------------------------------------------------------ Organism: EMBL File Server Address : netserv@embl.bitnet (2) Contents: EMBL (+ daily updates), SWISS-PROT, PDB DROMAP, ECD, ENZYME, EPD, LiMB, NGDD, PROSITE, SEQANALREF, TFD. Various Mac, VAX, UNIX, DOS software FASTA searches: search@embl.bitnet (2) Quicksearch (4) searches: quick@embl.bitnet (2) Contact : Rainer Fuchs fuchs@embl.bitnet ------------------------------------------------------------------------------- Organism: DDBJ E-Mail Network Server Address : netserv@flat.nig.ac.jp (2) Contents: DDBJ, GenBank (updated 2x daily), GenPep, EMBL(+updates), SWISS-PROT, PIR, PRF Keyword searches by author, journal, accession, and description Contact : Sanzo Miyazawa smiyazaw@nig.ac.jp ------------------------------------------------------------------------------- Organism: Genbank server Address : search@genbank.bio.net (2) for FASTA searches retrieve@genbank.bio.net for sequence retrieval Contact : consultant@genbank.bio.net (help with FASTA) retrieve-request@genbank.bio.net (help with retrieval) ------------------------------------------------------------------------------- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Bulletin boards +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------------------------------- Organism: BIOSCI newsgroups and archives Address : To subscribe: listserv@irlearn.bitnet (2) To send messages: newsgroup@irlearn.bitnet, where newsgroup is one of the following: 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 Example: AGEING@irlearn.bitnet Contact : Rob Harper harper@csc.fi ------------------------------------------------------------------------------- Organism: Photosynthesis researchers bulletin board Address : To subscribe: listserv@taunivm.bitnet (2) To send messages: photosyn@taunivm.bitnet Contact : Jonathan Marder marder@hujiagri.bitnet ------------------------------------------------------------------------------- Organism: GCG (3) software discussion group Address : To subscribe: listserv@utoronto.bitnet (2) To send messages: info-gcg@utoronto.bitnet Contact : John Cargill cargill@utoroci.bitnet or cargill@galen.oci.utoronto.ca ------------------------------------------------------------------------------- (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 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, NCBI) 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) GENPEPT GenBank translated protein db 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)