internet for the mol. biologist

Martin Leach leach at
Tue Oct 25 16:44:49 EST 1994

below is a list of mol biol ftp sites and servers

*     *     *     *     *     *     *     *     *     *     *     *     *     *
                     Molecular Biology FTP and Server List
                                 7 March 1991

                                Michael Gribskov
                              gribskov at

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 

      Software packages, databases, and smaller FTP sites
address                 contents    
responsible person/more information
+-----------------------------------------------------------------------------   PHYLIP phylogeny package v3.3

Joe Felsenstein*, joe at
+-----------------------------------------------------------------------------        PHYLIP phylogeny package v3.3          (officially sanctioned by author)

Alan Rogers, rogers at
+------------------------------------------------------------------------------         Codon usage tables for all major species 
( [.codon] )

Mike Cherry*, cherry at
+------------------------------------------------------------------------------        gm (gene modeler) package

Chris Fields*, cfields at
+------------------------------------------------------------------------------            AIMB (AI and                                  researchers database)

Lawrence Hunter*, hunter at
-------------------------------------------------------------------------------         USENET genbank software       

Ross Smith, smith at
+------------------------------------------------------------------------------                Delila sequence analysis system          (150 programs)    

Tom Schneider*, toms at
+------------------------------------------------------------------------------          FASTA database search         
(/public_access/fasta.shar)      program

William Pearson*, wrp at
      Larger FTP sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++         EMBL server                            EMBL (updated daily)
               SWISS-PROT (and updates), PDB
               DROMAP, ECD, ENZYME, EPD, LiMB, NGDD,
Rainer Fuchs            PROSITE, SEQANALREF, TFD. 
fuchs at embl.bitnet       PC, UNIX, Mac & VAX software
+------------------------------------------------------------------------------            GenBank, EMBL, DDBJ, PIR, SWISS-PROT,
               GENPEPT, LiMB
               Software: FLAT DB search/retrieval 
                    program for UNIX
Sanzo Miyazawa
smiyazaw at
+------------------------------------------------------------------------------            Genbank server           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 at      software
consultant at          On-line services
+------------------------------------------------------------------------------         IUBIO archive            Mac,VAX,Atari,DOS software
               DROMAP, EPD, LiMB, PROSITE, REBASE, 
Don Gilbert,                            TFD 
gilbertd at      Phylip
               Authorin program
-------------------------------------------------------------------------------       Molecular Biology Computer            Research Resource
Temple Smith,           PLSEARCH pattern db 
tsmith at      MASE 3.1 multiple sequence editor
+------------------------------------------------------------------------------           U Houston archive            Genbank sequence db
               PIR sequence db
Dan Davison,            UNIX,DOS,VMS,Mac software
dbd at        Cray software (future)
               BioMatrix archive
               Molecular evolution bb archive
+------------------------------------------------------------------------------          Biocomputing server          Biozentrum, Universitaet Basel
(/biology/EMBnet)       EMBL ( updated daily)
(/biology/databases)       ALU, DROMAP, ECD, ENZYME, EPD, LiMB,
                                        NGDD, PROSITE, REBASE, SEQANALREF,
               GCG (3) format codon usage tables

Reinhard Doelz,            BIOSCI Journal tables of contents
doelz at        Amos Bairoch*, bairoch at cgecmu51.bitnet
+------------------------------------------------------------------------------        Natl. Center for Biotech. Information          NCBI software

               Geninfo db documentation      
Scott Federhen,
federhen at     (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 at
+------------------------------------------------------------------------------                            Finnish State Supercomputer Center                           Center for Scientific Computing
(pub/sci/molbio)                        VAX, Unix, DOS, Mac software
                                        many non-biological applications
Rob Harper, harper at
      Server sites
bioserve%genome at (2)     Los Alamos National Laboratory server
               Genbank documentation         
Michael Cinofsky,       software archive (future)
michael%domain at 
fileserv at gunbrf.bitnet (2)    PIR server           
               PIR, NBRF Nucleic, Genbank, EMBL 

Dr. John S. Garavelli, garavell at gunbrf.bitnet      
Ms. Kathryn Sidman,   pirmail at gunbrf.bitnet
gene-server at (1)      U Houston gene server         
               Genbank sequence db
gene-server-management at  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

               BIO-JRNL, BIOMATRX, BIO-SOFT, CHROM-22, 
               ORG, GNOME-PR, METHODS, MOL-EVOL, 
               POP-BIO, PROTEINS, SCI-RES
Rob Harper, harper at     (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
netserv at 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 at embl.bitnet (2)        FASTA searches
quick at embl.bitnet (2)         Quicksearch (4) searches
Rainer Fuchs, fuchs at embl.bitnet
netserv at  (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 at       journal, accession, and description
pythia at  (2)      Alu sequence identification server

Aleksandar Milosavljevic
pythia-admin at 
milosav at
               Genbank  server            
search at (2)    FASTA searches 
retrieve at      Sequence retrieval         

genbank at
consultant at    (help with FASTA)
retrieve-request at (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

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)

Good luck compiling the book...
let me know if you want any more info 

Martin Leach


.....          Martin Leach                Email:leach at 
   _|_______      Dept. of Pharmacology       Phone: (617) 638-5323        
   /  o    /      Boston Univ. School of Med. Fax:   (617) 638-4329         
 _/   |-  /__==/  80 E. Concord St. (L603)
(TURBODOZER) \_   Boston MA 02118            "Not the old underpants
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                                             " -BLACKADDER  

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