List of molecular biology FTP servers / Release 1.50

Amos Bairoch BAIROCH at cmu.unige.ch
Mon Aug 2 16:21:48 EST 1993


==============================================================================
Name   : serv_ftp.txt
Version: 1.50 / July 30, 1993
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
         bairoch at cmu.unige.ch
==============================================================================

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FEEDBACK IN THE FORM OF CORRECTIONS, ADDITIONS, ETC ARE MORE THAN WELCOME !!! 
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A) INTRODUCTION
===============

  A1) General introduction
  ------------------------

This document describes the various sources  of databases and software for
molecular biologists that are  publicly available on the internet computer
network.  This  documents restricts itself to describing sites that allows
the transfer  of files by what  is known as anonymous "ftp" (File transfer
protocol).  We do not describe here the BIOSCI electronic newsgroup system
or the other bulletin  boards  that  are available to molecular biologist,
nor do we describe email servers.  These  services  are  described  in the
following documents:

   serv_ema.txt: For a list of molecular biology email servers.
   serv_bbo.txt: For a list of bulletin boards services for molecular
                 biologists.
  

Acknowledgment: the information contained in this document  come from many
                different sources; but we want to partcularily acknowledge
                the work of Michael Gribskov (gribskov at sdsc.edu) which, in 
                December 1990  and March 1991  produced  a  compilation of
                server sites; Bob Harper (harper at convex.csc.fi) for having
                forwarded me information from various sources.

  A2) Some tips
  -------------

1) On all the FTP servers listed in this document you should login using the
   user name "anonymous" and using your full E-mail address  as the password
   (example: smith at somemachine.somenet.somedomain).

2) There are, in general, files with names such  as  "read.me", "readme.txt"
   or "readme" at different directory levels on many FTP servers. If you are
   using a server  for the first  time,  it is a good idea to first transfer
   these files and to read them before transferring other files.  Note  that
   you can generally do that  without interupting the connection by shelling
   to your operating system:

   a) Type "get readme.txt" to transfer the file on your local system.
   b) Once the file has been transferred type "!"   (if your local system is
      running DOS or UNIX system) or "SPAWN"  (if your local system is a VAX
      VMS). You will then see your usual operating system prompt.
   c) You can then view the file with your favorite file viewer or editor.
   d) To get back  in the  FTP  program type  "exit"  (on DOS or on UNIX) or
       "LOGOUT" (on a VAX VMS).

   Note: on VAX VMS there is a shortcut to the above procedure, you can type:

       GET readme.txt TT:
 
   This displays the file directly to the terminal (but  it does not transfer
   it to your computer, so if you want to keep a local copy you should follow
   the procedure described above).

3) When transferring binary files such  as program files or compressed  files
   (with the .Z file extension for example), do  not  forget to first set the
   transfer mode to "binary".  Do not also forget to reset it back to "ASCII"
   if you later, in the same session,  want to transfer text files.  However,
   if your system is running the same operating system than that of the  host
   server, you can transfer all files, even text files, in binary mode.


  A3) Release history
  -------------------

Release 0.90 / January 6, 1993
        1.00 / February 1, 1993
        1.10 / March 1, 1993
        1.20 / April 3, 1993
        1.30 / May 12, 1993
        1.40 / May 27, 1993
        1.50 / July 30, 1993

==============================================================================

B) DATABASES
============

  B1) Databases abbreviations
  ---------------------------

db          Database

5S_RNA      Berlin 5S rRNA db
AIDS-db     Human Retroviruses and HIV viruses compilation of sequences
AIMB-db     Artificial intelligence and molecular biology researchers db
Alu         Alu Sequence db
Blocks      Protein blocks db
Codon       Codon usage tables for the GCG software package
CpGIsle     CpG islands in the human genome db
CCSD        Complex Carbohydrate Structure db
CUTG        Codon usage tables for all major species
DDBJ        DNA Data Bank of Japan
DSSP        Dictionary of Secondary structure of proteins
ECD	    Escherichia coli db
EMBL	    European Molecular Biology Laboratory nucleotide sequence db
Enzyme      Enzymes nomenclature db
EPD         Eukaryotic Promoter db
EST-db      Expressed Sequence Tag db
FANS_Ref    Functional Analysis of Nucleotide Sequences bibliography
FlyBase     Drosophila Genetic Maps db
GDB         Human Genome db
GenBank     GenBank nucleic acid db
GenPept     Automatic translation of GenBank CDS into protein sequences
HAEMB       Haemophilia B mutations db
Jour_TOC    Table of contents of some biomolecular journals
Kabat       Sequences of proteins of immunological interest
LiMB        Listing of Molecular Biology databases
LISTA       Compilation of nucleotide seq. encoding prot. from Saccharomyces
NGDD        Normalized Gene Designation db
OMIM        Online Mendelian Inheritance in Man
PDB         Protein Data Bank (3D structures)
PIR	    Protein Information Resource (NBRF protein sequence db)
PKCDD       Protein kinases catalytic domain db
Plsearch    Automatically generated protein sequence patterns db
Prosite     Dictionary of Protein Sites and Patterns
RDP         Ribosomal Database project
Rebase      Restriction Enzymes db
RepBase     Prototypic sequences for human repetitive DNA
SeqAnalRef  Sequence analysis bibliography
Small_RNA   Compilation of small RNA sequences
Swiss-Prot  Swiss-Prot protein sequence db
T4-Phage    Bacteriophage T4 genome sequence files
TFD         Transcription Factors Relational db
TransTerm   Translational Termination signal db
tRNA        Compilation of tRNA sequences and sequences of tRNA genes


  B2) Major FTP servers for databases
  -----------------------------------

Organiz. : National Center for Biotechnology Information (NCBI)
Name     : NCBI repository
Address  : ncbi.nlm.nih.gov (130.14.20.1)
Contact  : Scott Federhen; federhen at ncbi.nlm.nih.gov

Organiz. : European Molecular Biology Laboratory
Name     : EMBL Anonymous Ftp Server
Address  : ftp.embl-heidelberg.de (192.54.41.33)
Contact  : Rainer Fuchs; nethelp at embl-heidelberg.de

Organiz. : Weizmann Institute of Science (EMBnet Israel national node)
Name     : DNA and protein sequence analysis (DAPSAS) ftp server
Address  : sunbcd.weizmann.ac.il (132.76.64.79)
Contact  : Jaime Prilusky; lsprilus at weizmann.weizmann.ac.il

Organiz. : Basel Biozentrum Biocomputing server (EMBnet SWISS national node)
Name     : Basel EMBNet ftp server
Address  : bioftp.unibas.ch (131.152.8.1)
Contact  : Reinhard Doelz; doelz at urz.unibas.ch

Organiz. : National Institute of Genetics (Japan)
Name     : National Institute of Genetics ftp server
Address  : ftp.nig.ac.jp (133.39.16.66)
Contact  : Yoshihiro Ugawa; yugawa at genes.nig.ac.jp


+-------------------------+--------+------+------+-------+-------+
|  Name                   |  NCBI  | EMBL | Weiz | Basel | Japan |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  DDBJ                   |        |      |      |       | Yes   |
|  EMBL                   |        |  Yes |  Yes |  Yes  | Yes   |
|  GenBank                |   Yes  |      |  Yes |       | Yes   |
|  SWISS-PROT             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  PIR                    |        |      |  Yes |  Yes  | Yes   |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  5S_rRNA                |        |  Yes |  Yes |  Yes  |       |
|  AIDS-db                |   Yes  |      |  Yes |       |       |
|  AIMB-db                |   Yes  |      |  Yes |       |       |
|  Alu                    |        |  Yes |  Yes |  Yes  |       |
|  Blocks                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  CpGIsle                |        |  Yes |  Yes |  Yes  |       |
|  CCSD                   |   Yes  |      |      |  Yes  |       |
|  CUTG                   |        |  Yes |  Yes |  Yes  | Yes   |
|  DSSP                   |        |  Yes |  Yes |       |       |
|  ECD                    |        |  Yes |  Yes |  Yes  | Yes   |
|  EcoSeq/Map/Gene        |   Yes  |      |      |       |       |
|  Enzyme                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EPD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EST-db                 |   Yes  |      |      |  Yes  |       |
|  FANS-Ref               |        |  Yes |  Yes |  Yes  |       |
|  FlyBase                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  HAEMB                  |        |  Yes |  Yes |  Yes  |       |
|  HLA                    |        |  Yes |  Yes |  Y


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