From: BAIROCH@cmu.unige.ch (Amos Bairoch)
Newsgroups: bionet.announce
Subject: List of molecular biology FTP servers (Preliminary edition).
Date: 7 Jan 93 01:30:03 GMT


==============================================================================
Name   : serv_ftp.txt
Version: 0.9 / January 6, 1993
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
         bairoch@cmu.unige.ch
==============================================================================

-----------------------------------------------------------------------------
    THIS IS A PRELIMINARY VERSION OF THIS DOCUMENT, FEEDBACK IN THE FORM
            OF CORRECTIONS, ADDITIONS, ETC ARE MORE THAN WELCOME !!! 
-----------------------------------------------------------------------------

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@sdsc.edu) which, in 
                December 1990  and March 1991  produced  a  compilation of
                server sites; Bob Harper (harper@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@somesite.somenet.node).

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).

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 0.9 / January 6, 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
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
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
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
tRNA        Compilation of tRNA sequences and sequences of tRNA genes


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

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

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

Organism : 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  : James Prilusky; lsprilus@weizmann.weizmann.ac.il

Organism : 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@urz.unibas.ch

Organism : 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@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   |
|  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  |       |
|  Jour_TOC               |   Yes  |      |      |  Yes  |       |
|  Kabat                  |   Yes  |      |  Yes |       |       |
|  LiMB                   |   Yes  |  Yes |  Yes |  Yes  |       |
|  NGDD                   |   Yes  |      |      |  Yes  |       |
|  PKCDD                  |   Yes  |  Yes |  Yes |  Yes  |       |
|  Prosite                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Rebase                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Repbase                |   Yes  |      |      |  Yes  |       |
|  SeqanalRef             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Small_RNA              |        |  Yes |  Yes |  Yes  |       |
|  T4-Phage               |   Yes  |      |  Yes |  Yes  |       |
|  TFD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  tRNA                   |        |  Yes |  Yes |  Yes  |       |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+------ +


  B3) Other FTP servers for databases
  -----------------------------------

Organism : University of Geneva / Medical Biochemistry and University Hospital
Name     : ExPASy server
Address  : expasy.hcuge.ch (129.195.254.61)
Databases: Enzyme, EPD, Prosite, SeqanalRef, SWISS-PROT
Contact  : Amos Bairoch; bairoch@cmu.unige.ch

Organism : Department of Molecular biology / Massachussetts General Hospital
Address  : frodo.mgh.harvard.edu (132.183.190.10)
Databases: EMBL, Codon
Contact  : Mike Cherry; cherry@frodo.mgh.harvard.edu

Organism : University of Houston Gene-Server
Address  : ftp.bchs.uh.edu (129.7.2.43)
Databases: PIR
           Directory: /pub/gene-server/pir
Contact  : Dan Davison; dbd@theory.bchs.uh.edu

Organism : Indiana University / Biology Department
Name     : IuBio archive for biology
Address  : ftp.bio.indiana.edu (129.79.224.25)
Databases: FlyBase and various other fly databases and stock lists.
Contact  : Don Gilbert; archive@bio.indiana.edu

Organism : ?
Address  : ftp.tigr.org (192.207.234.10)
Databases: EST-db
Contact  : ?

Organism : National Library of Medicine
Address  : lhc.nlm.nih.gov (130.14.1.128)
Databases: AIMB-db
           Directory= /pub/aimb-db
Contact  : Lawrence Hunter; hunter@nlm.nih.gov

Organism : Molecular Biology Computer Research Resource (MBCRR)
Address  : mbcrr.harvard.edu (134.174.51.4) 
Databases: Plsearch
           Directory= /MBCRR-Package
Contact  : Temple Smith; tsmith@mbcrr.harvard.edu 

Organism : Human Genome Data Base / Johns Hopkins University
Address  : mendel.welch.jhu.edu (128.220.59.42)
Databases: GDB, OMIM.
Contact  : GDB User Support; help@welch.jhu.edu

Organism : Protein Data Bank (PDB)
Address  : pdb.pdb.bnl.gov (130.199.144.1)
Databases: PDB
Contact  : skora@bnl.gov.

Organism : The Salk Institute for Biological Studies
Address  : salk-sc2.sdsc.edu (192.31.153.12)
Databases: PKCDD
Contact  : Anne Marie Quinn; quinn@salk-sc2.sdsc.edu

Organism : New England BioLabs (NEB)
Address  : vent.neb.com (192.138.220.2)
Databases: Rebase
           Directory= /pub/rebase
Contact  : Dana Macelis; macelis@neb.com

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

C) SOFTWARE
===========

  C1) Generalities
  ----------------

There are a few servers (see section C2)   that  store a variety of software
packages for molecular biology users.  These servers offer you many packages
for DOS, Mac, Unix, or VMS.  In addition to these big software "supermarket"
there are quite a number of sites that provide  one or two specific packages
or programs  which  have  been  writen by the person(s) that  work  on  that
particular computer site. In general these  programs are also available from
the "supermarkets", but if you  want to be sure to get the latest release of
a software package, it is always  better to get it from the people who wrote
it !!

+++ Will add a section on compression scheme and software +++


  C2) Major FTP servers for software
  ----------------------------------

Organism : European biology Molecular Laboratory
Name     : EMBL Anonymous Ftp Server
Address  : ftp.embl-heidelberg.de (192.54.41.33)
Contents : Various Mac, VAX, DOS, and UNIX software
           DOS and VAX software are stored as uuencoded (.UUE) files.
           Mac software are stored as binhexed (.HQX) files.
           UNIX software are stored as archive (tar) files compressed (.Z).
           Directory= /pub/software/dos  or /pub/software/mac or
                      /pub/software/unix or /pub/software/vax
Contact  : Rainer Fuchs; nethelp@embl-heidelberg.de
Status   : Tested (30 Oct 1992).


Organism : 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)
Contents : This server provides a "mirror" image of the content of the EMBL
           file server (described above), but as the access to EMBL can  be
           very slow, you can use  this  server as an alternative source of
           all the software listed above.
Contact  : James Prilusky; lsprilus@weizmann.weizmann.ac.il
Status   : Tested (30 Sep 1992).


Organism : Indiana University / Biology Department
Name     : IuBio archive for biology
Address  : ftp.bio.indiana.edu (129.79.224.25)
Contents : Various Mac, VAX, Atari, DOS software
	   Authorin data entry program
  	   PHYLIP phylogeny package
Contact  : Don Gilbert; gilbertd@cricket.bio.indiana.edu 


Organism : University of Houston
Name     : University of Houston Gene-Server
Address  : ftp.bchs.uh.edu (129.7.2.43)
Contents : Various Mac, VAX, DOS, and UNIX software
Contact  : Dan Davison; dbd@theory.bchs.uh.edu
Status   : Tested (30 Oct 1992).


Organism : National Institute of Genetics (NIG) (Japan)
Name     : National Institute of Genetics ftp server
Address  : ftp.nig.ac.jp (133.39.16.66)
Contents : Mac software: Amplify; DNAnalyze; DNAstacks; MacPattern;
           MacPlasmap; MacMolecule; NCSA GelReader; Phylip; Speakquencer;
           Treedraw
           DOS software: Phylip
           UNIX software: Phylip; ProSearch
Contact  : Yoshihiro Ugawa; yugawa@genes.nig.ac.jp
Status   : Tested (5 Oct 1992).


  C3) Servers for specific software packages
  ------------------------------------------

-------------------------------------------------------------------------------
Organism: National Center for Biotechnology Information (NCBI)
Address : ncbi.nlm.nih.gov (130.14.20.1)
Programs: Name=blast; Desc=Basic Local Alignment Search Tool; OS=UNIX
          Directory= /pub/blast
          Name=Macaw; Desc=MS-Windows multiple sequence alignment program;
          OS=DOS    
          Directory= /pub/macaw
          NCBI Entrez
          Directory= /entrez
          GenInfo Software Toolbox
          Directory= /toolbox
          Name=nrdb; Desc=Program to generate the NCBI ""nonredundant""
          databases; OS=UNIX
          Directory= /pub/nrdb
Contact : Scott Federhen; federhen@ncbi.nlm.nih.gov 
Status  : Tested (30 Sep 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Address : evolution.genetics.washington.edu (128.95.12.41)
Programs: Name=PHYLIP; Desc=Phylogeny inference package;
          Directory= /pub
Contact : Joe Felsenstein [*]; joe@genetics.washington.edu
Status  : Tested (30 Sep 1992).
-------------------------------------------------------------------------------

------------------------------------------------------------------------------
Address : anthro.utah.edu (128.110.192.93)
Programs: Name=PHYLIP; Desc=Phylogeny inference package;
          Directory= /pub
Contact : Alan Rogers; rogers@anthro.utah.edu
Status  : Tested (30 Oct 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Address:  relay.cs.utoronto.ca (128.100.3.6 or 128.100.1.105)
Programs: Name=RAMHA; Desc=random mutagenesis simulation software;
Contact:  David P. Siderovski [*]; siderovski@galen.oci.utoronto.ca
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Address : ccu.umanitoba.ca (130.179.16.8)
Programs: Name=XYLEM; Desc=Molecular Database package;
          Directory= /psgendb
          Name=FSAP; Desc=Sequence Analysis;
          Directory= /psgendb
Contact : Brian Fristensky [*]; frist@ccu.umanitoba.ca
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: University of Geneva Switzerland
Address : expasy.hcuge.ch (129.195.254.61)
Programs: Name=ProMod; Desc=3D modeling software; OS=UNIX;
          Directory= /pub/ProMod
Contact : Manuel Peitsch [*]; peitsch@ulbio1.unil.ch
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: New Mexico State University
Address : haywire.nmsu.edu (128.123.001.032)
Programs: Name=gm; Desc=Gene modeler software package; OS=UNIX;
          Directory= /gm
Contact : Chris Fields [*]; cfields@nmsu.edu
Status  : Tested (1 Oct 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: NCI/FCRDC
Address : ncifcrf.gov (129.43.2.10)
Programs: Name=Delila; Desc=sequence analysis system (150 programs including
          those for creating sequence logos). Portable Pascal and C;
          Directory= /pub/delila
Contact : Tom Schneider [*]; toms@ncifcrf.gov
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: University of Virginia
Address : uvaarpa.virginia.edu (128.143.2.7)
Programs: Name=FASTA; Desc=database search program; OS=UNIX and DOS;
          Directory= /pub/fasta
Contact : William Pearson [*]; wrp@virginia.edu
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: Department of Molecular biology / Massachussetts General Hospital
Address : frodo.mgh.harvard.edu	(132.183.190.10)
Programs: Desc=Zuker's suboptimal RNA folding package; OS=VMS;
          Directory= [.VAX]
Contact : Mike Cherry; cherry@frodo.mgh.harvard.edu
Status  : Tested (30 Sep 1992).
-------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: Harvard/M.I.T. Division of Health Sciences and Technology and the
          Harvard Division on Aging
Address : amber.mgh.harvard.edu (132.183.190.26)
Programs: Name=sg2iq; Desc=Utility program for converting images of gels
          created by software for a Hewlett Packard desktop scanner (tiff
          files) to the format expected by the ImageQuant gel analysis
          software from Molecular Dynamics; OS=DOS;
          Directory= [.PC]
Contact : Dave Rigney [*]; david@astro.bih.harvard.edu
Status  : Tested (27 Oct 1992).
-------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organism: University of Illinois at Urbana-Champaign
Address : ftp.ncsa.uiuc.edu (141.142.20.50)
Programs: Name=NCSA GelReader; Desc=Measurement of DNA length from gels;
          OS=Mac;
          Directory= /Mac/GelReader
          Name=NCSA ContigAsm; Desc=Reads NCSA GelReader files and assemble
          contigs; OS=Mac;
          Directory= /Mac/ContigAsm
Contact : Jennie File [*]; jfile@ncsa.uiuc.edu
Status  : Tested (2 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: Department of Mathematics / Stanford University
Address : gnomic.stanford.edu (36.120.0.19)
Programs: Name=SAPS; Desc=Statistical analysis of protein sequences; OS=UNIX;
          Directory= /pub
Contact : Voker Brendel [*]; volker@gnomic.stanford.edu
Status  : Tested (2 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: Department of Biochemistry / Stanford University
Address : cmgm.stanford.edu (36.96.0.200)
Programs: Desc=Series of BLAST and FASTA scripts both for users and for Unix
          systems administrators who prepare BLAST indexes available via
          anonymous FTP. The database indexing scripts are specific for those
          who use the IntelliGenetics suite;
          Directory= /pub/IGdb
Contact : Klinger; klingler@cmgm.stanford.edu
Status  : Tested (29 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: Molecular Biology Computer Research Resource (MBCRR)
Address : mbcrr.harvard.edu (134.174.51.4) 
Programs: Name=ALIGN/LOCAL; Desc=Optimally aligns a pair of sequences;
          Directory= /MBCRR-Package
          Name=DASHER3; Desc=High-speed k-tuple/hash database search tool
          Directory= /MBCRR-Package
          Name=DYNAMIC; Desc=Match one or more short sequences against a
          longer sequence using a fast dynamic programming algorithm
          Directory= /MBCRR-Package
          Name=GGREP; Desc=Performs "regular expression" pattern searches of
          nucleic acid or protein sequences using the GNU-Emacs regular
          expression handler
          Directory= /MBCRR-Package
  	  Name=MASE; Desc=Multiple sequence editor
          Directory= /MBCRR-Package
          Name=PIMA; Desc=Pattern-Induced Multiple-sequence Alignment program
          Directory= /MBCRR-Package
Contact : Temple Smith [*]; tsmith@mbcrr.harvard.edu 
Status  : Tested (1 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: New England BioLabs (NEB)
Address : vent.neb.com (192.138.220.2)
Programs: Name=detect; Desc=Program that locates errors in DNA sequences;
          OS=UNIX;
          Directory= /pub/detect
Contact : Rich Roberts [*]; roberts@neb.com
Status  : Tested (1 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: Intelligenetics Inc.
Address : net.bio.net (134.172.2.69)
Programs: Name=Authorin; Desc=Program for preparing sequence data for
          submission to the nucleic acid and protein data banks;
          OS=Mac and DOS;
          Directory= /pub/mac/authorin  or /pub/dos/authorin
Contact : Dave Kristofferson; kirstoff@net.bio.net
Status  : Tested (27 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organism: CSIRO Division of Entomology / Canberra Australia
Address : spider.ento.csiro.au (138.44.23.1)
Programs: Name=DELTA; Desc=DEscriptive Language for TAxonomy;
          OS=DOS and UNIX;
          Directory= /delta
Contact : Mike Dallwitz; delta@ento.csiro.au
Status  : Tested (27 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Address : groucho.cs.psu.edu (130.203.2.10)
Programs: Name=LAV and LAD; Desc=Software tools for analyzing pairwise
          alignments of long sequences; OS=UNIX;
          Directory= /lav
          Name=TNB; Desc=Software tools for multiple alignment and
          visualization; OS=UNIX;
          Directory= /TNB
          Desc=Software for aligning two sequences within a specified
          diagonal band; OS=UNIX or DOS;
          Directory= /band
Status  : Tested (30 Oct 1992).
------------------------------------------------------------------------------

==============================================================================
=End=of=document==============================================================