internet for the mol. biologist

Martin Leach leach at mbcrrc.bu.edu
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 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 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
+------------------------------------------------------------------------------
frodo.mgh.harvard.edu         Codon usage tables for all major species
132.183.190.10 
( [.codon] )

Mike Cherry*, cherry at frodo.mgh.harvard.edu
+------------------------------------------------------------------------------
haywire.nmsu.edu        gm (gene modeler) package  
128.123.001.032

Chris Fields*, cfields at nmsu.edu
+------------------------------------------------------------------------------
lhc.nlm.nih.gov            AIMB (AI and mol.bio. 
130.14.1.128                                  researchers database)
(/pub/aimb-db)

Lawrence Hunter*, hunter at nlm.nih.gov
-------------------------------------------------------------------------------
mcclb0.med.nyu.edu         USENET genbank software       

Ross Smith, smith at mcclb0.med.nyu.edu
+------------------------------------------------------------------------------
ncifcrf.gov                Delila sequence analysis system 
129.43.1.11          (150 programs)    
(/pub/delila)

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 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 at 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 at 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 at genbank.bio.net      software
consultant at 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 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)       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 at urz.unibas.ch        Amos Bairoch*, bairoch at cgecmu51.bitnet
+------------------------------------------------------------------------------
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)           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 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 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           
               PIR, NBRF Nucleic, Genbank, EMBL 

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)
               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 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 at flat.nig.ac.jp       journal, accession, and description
+------------------------------------------------------------------------------
pythia at cis.ucsc.edu  (2)      Alu sequence identification server

Aleksandar Milosavljevic
pythia-admin at cis.ucsc.edu 
milosav at cis.ucsc.edu
+------------------------------------------------------------------------------
               Genbank  server            
search at genbank.bio.net (2)    FASTA searches 
retrieve at genbank.bio.net      Sequence retrieval         

genbank at genbank.bio.net
consultant 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)


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 mbcrrc.bu.edu 
   _|_______      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
                  USA                         on your head....WIBBLE
                                             " -BLACKADDER  





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