internet for the mol. biologist

Francis Ouellette francis at borduas.nlm.nih.gov
Wed Oct 26 10:16:32 EST 1994


here is a better list of FTP addresses for Molecualr Biology.

regards,

francis

--
| B.F. Francis Ouellette  
|
| francis at ncbi.nlm.nih.gov   


==============================================================================
Name   : serv_ftp.txt
Version: 3.00 / September 23, 1994
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry
         University of Geneva / Switzerland
         Email to: bairoch at cmu.unige.ch
==============================================================================

-----------------------------------------------------------------------------
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 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) Where can you find this file and the other serv_xxx files
  -------------------------------------------------------------

The latest version of the serv_ema.txt, serv_ftp.txt and serv_bbo.txt files
are always available, by anonymous FTP, on the following server:

    expasy.hcuge.ch  (129.195.254.61)

These files are in the directory:

    /databases/info
   
You will also find lots of other interesting information files including the
help file of most servers (these files have the extension '.srv') as well as
files describing software packages ('.sof'),  databases ('.dba'),  FTP sites
('.ftp')  and general information files ('.txt').

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

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
ALN          NBRF protein sequence alignments 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
dbEST        NCBI Expressed Sequence Tag db
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
FANS_Ref     Functional Analysis of Nucleotide Sequences bibliography
FlyBase      Drosophila Genetic Maps db
GCRDb        G Protein Coupled Receptor db
GDB          Human Genome db
GenBank      GenBank nucleic acid db
GenPept      Automatic translation of GenBank CDS into protein sequences
HAEMB        Haemophilia B mutations db
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
NRL_3D       NBRF protein sequence from PDB db
Omega        OMEGA data bank (3D structures)
OMIM         Online Mendelian Inheritance in Man
Owl          OWL merged protein db
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
Prints       Prints db of protein fingerprints
Prosite      Dictionary of Protein Sites and Patterns
RDP          Ribosomal Database project
Rebase       Restriction Enzymes db
RepBase      Prototypic sequences for repetitive DNA
SBASE        Proteins sequence domains db
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

[*] Databases flagged with "*" have not been updated for more than 12 months


  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 Bioinformatics Institute / Hinxton / UK
Name     : EBI Anonymous Ftp Server
Address  : ftp.ebi.ac.uk (193.62.196.6)
Contact  : Peter Stoehr; nethelp at ebi.ac.uk

Organiz. : Weizmann Institute of Science (EMBnet Israel national node)
Name     : DNA and protein sequence analysis (DAPSAS) ftp server
Address  : bioinformatics.weizmann.ac.il (132.76.55.12)
Contact  : Chaim Prilusky; lsprilus at weizmann.weizmann.ac.il

Organiz. : National Institute of Genetics (NIG) (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

Organiz. : Genome Database Network in Japan (GDBnetJP)
Name     : GDBnet
Address  : ftp.gdbnet.ad.jp (160.74.32.10)


+-------------------------+--------+------+------+----------+--------+
|  Name                   |  NCBI  | EBI  | Weiz | NIG Jpn  | GDBNet |
+-------------------------+--------+------+------+----------+--------+
|                         |        |      |      |          |        |
|  DDBJ                   |        |      |      | Yes      |        |
|  EMBL                   |        |  Yes |  Yes | Yes      | Yes    |
|  GenBank                |   Yes  |      |  Yes | Yes      | Yes    |
|  SWISS-PROT             |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  PIR                    |   Yes  |      |  Yes | Yes      | Yes    |
|                         |        |      |      |          |        |
+-------------------------+--------+------+------+----------+--------+
|                         |        |      |      |          |        |
|  5S_rRNA                |        |  Yes |  Yes |          | Yes    |
|  AIDS-db                |   Yes  |      |  Yes |          |        |
|  AIMB-db                |   Yes  |      |  Yes |          |        |
|  ALN                    |   Yes  |      |      |          |        |
|  Blocks                 |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  CpGIsle                |        |  Yes |  Yes |          | Yes    |
|  CCSD                   |   Yes  |      |      |          | Yes    |
|  CUTG                   |        |  Yes |  Yes | Yes      | Yes    |
|  dbEST                  |   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    |
|  FANS-Ref               |        |  Yes |  Yes |          | Yes    |
|  FlyBase                |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  GCRDb                  |   Yes  |      |      |          |        |
|  HAEMB                  |        |  Yes |  Yes |          | Yes    |
|  HLA                    |        |  Yes |  Yes |          | Yes    |
|  HSSP                   |        |  Yes |  Yes |          |        |
|  Kabat                  |   Yes  |  Yes |  Yes |          | Yes    |
|  LiMB                   |   Yes  |  Yes |  Yes |          | Yes    |
|  LISTA                  |   Yes  |  Yes |  Yes |          | Yes    |
|  NGDD                   |   Yes  |      |      |          | Yes    |
|  NRL-3D                 |   Yes  |      |      |          | Yes    |
|  PKCDD                  |   Yes  |  Yes |  Yes |          | Yes    |
|  Prints                 |        |  Yes |  Yes |          |        |
|  Prosite                |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  Rebase                 |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  Repbase                |   Yes  |  Yes |  Yes |          | Yes    |
|  SBASE                  |        |  Yes |  Yes |          | Yes    |
|  SeqAnalRef             |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  Small_RNA              |        |  Yes |  Yes |          | Yes    |
|  T4-Phage               |   Yes  |      |  Yes |          | Yes    |
|  TFD                    |   Yes  |  Yes |  Yes | Yes      | Yes    |
|  TransTerm              |        |  Yes |  Yes |          | Yes    |
|  tRNA                   |        |  Yes |  Yes |          | Yes    |
|                         |        |      |      |          |        |
+-------------------------+--------+------+------+----------+--------+


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

Organiz. : 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
           Directory: /databases
Contact  : Amos Bairoch; bairoch at cmu.unige.ch

Organiz. : Department of Molecular biology / Massachussetts General Hospital /
           Boston / USA
Address  : frodo.mgh.harvard.edu (132.183.190.10)
Databases: Codon
Contact  : Mike Cherry; cherry at frodo.mgh.harvard.edu

Organiz. : Renal Unit / Massachusetts General Hospital / Boston / USA
Address  : receptor.mgh.harvard.edu (132.183.143.16)
Databases: GCRDb
           Directory= /pub/GCRDb
Contact  : Lee F. Kolakowski Jr; lfk at receptor.mgh.harvard.edu

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

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

Organiz. : Biology Department / Indiana University / USA
Name     : IuBio archive for biology
Address  : ftp.bio.indiana.edu (129.79.224.25)
Databases: FlyBase and various other fly databases and stock lists.
           Archive of the BIOSCI newsgroup postings (In directory:
           /usenet/bionet).
Contact  : Don Gilbert; gilbertd at cricket.bio.indiana.edu 

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

Organiz. : Human Genome Data Base / Johns Hopkins University / USA
Address  : ftp.gdb.org (192.239.77.3)
Databases: GDB, OMIM.
Contact  : GDB User Support; help at gdb.org

Organiz. : Protein Data Bank (PDB)
Address  : ftp.pdb.bnl.gov (130.199.144.1)
Databases: PDB
Contact  : skora at bnl.gov.

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

Organiz. : Frederick Biomedical Supercomputer Center (NCI-FCRDC) / Frederick /
           Maryland / USA
Address  : ftp.ncifcrf.gov (129.43.1.11)
Databases: GenPept
           Directory= /pub/genpept
Contact  : Mark A. Gunnell; gunnell at ncifcrf.gov

Organiz. : Pittsburgh Supercomputing Center (PSC) / USA
Address  : ftp.psc.edu (128.182.62.148)
Databases: GenBank
           Directory= /biomed/genbank/annotated
Contact  : Alex Ropelewski; ropelews at psc.edu

Organiz. : Ribosomal Database Project / University of Illinois / USA
Address  : rdp.life.uiuc.edu (128.174.86.14)
Databases: RDP
           Directory= /pub/RNAdb
Contact  : rdp at phylo.life.uiuc.edu

Organiz. : BIOSCI at IntelliGenetics / Mountain View / USA
Address  : net.bio.net (134.172.2.69)
Databases: BIOSCI documents (including FAQ)
           Directory= /pub/BIOSCI
Contact  : Dave Kristofferson; kristoff at net.bio.net

Organiz. : Protein Science
Address  : ftp.uci.edu (128.200.15.20)
Databases: Table of contents, abstracts and other documents from the journal
           Protein Science.

Organiz. : Stanford university human genome mapping center / Stanford / USA
Address  : toolik.stanford.edu (36.159.0.5)
Databases: High-resolution physical maps of human chromosome 4.
Contact  : hgmcinfo at camis.stanford.edu

Organiz. : SERC Daresbury / UK
Address  : s-ind2.dl.ac.uk ()
Databases: Various databases and software package. Provides part of what is
           found on the EMBL and INN servers.
Contact  : Alan Bleasby; ajb at s-ind2.dl.ac.uk

Organiz. : ICGEB / Trieste / Italy
Address  : ftp.icgeb.trieste.it (140.105.9.1)
Databases: SBASE
           Directory= /pub/sbase2
Contact  : Zsolt Hatsagi; hatsagi at icgeb.trieste.it 

Organiz. : Laboratoire de Biometrie, Genetique et Biologie des Populations /
           Lyon / France
Address  : biom3.univ-lyon1.fr (134.214.100.42)
Databases: HOVERGEN (database of homologous vertebrate genes).
           Directory= /pub/hovergen
Contact  : Laurent Duret; duret at biomserv.univ-lyon1.fr

Organiz. : Departement des Macromolecules Biologiques / Laboratoire de
           Mineralogie - Cristallographie / Universite Pierre et Marie Curie /
           Paris / France
Address  : genome.inserm-vjf.fr (192.134.32.20)
Databases: OMEGA (database of protein structural information).
           Directory= /pub/omega
Contact  : Michel T. Semertzidis; semerz at lmcp.jussieu.fr

Organiz. : INRA Toulouse / France
Address  : dune.toulouse.inra.fr (192.93.80.7)
Databases: ProDom (database of protein domains).
           Directory= /pub/prodom
Contact  : Daniel Kahn; dkahn at toulouse.inra.fr

Organiz. : Laboratoire de Regulation de l'Expression Genetique / Institut
           Pasteur / France
Address  : radium.jussieu.fr (134.157.56.1)
Databases: Colibri (E.coli genome database)
           Directory= /pub/colibri
Contact  : bunny at radium.jussieu.fr

Organiz. : Institute of Protein Research / Russia Academy of Sciences / Russia
Address  : imb.mb.free.net (193.233.6.1)
Databases: FANS-REF (bibliography)
           Directory= /biblio
Contact  : misha at ib.mb.free.net

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

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

  C1) General remarks
  -------------------

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 "supermarkets"
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  at  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 !!


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

Organiz. : European Bioinformatics Institute / Hinxton / UK
Name     : EBI Anonymous Ftp Server
Address  : ftp.ebi.ac.uk (193.62.196.6)
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  : Peter Stoehr; nethelp at ebi.ac.uk
Status   : Tested (30 Oct 1992).


Organiz. : Weizmann Institute of Science (EMBnet Israel national node)
Name     : DNA and protein sequence analysis (DAPSAS) FTP server
Address  : bioinformtics.weizmann.ac.il (132.76.55.12)
Contents : This server provides a "mirror" image of the content of the EBI
           file server (described above).
Contact  : Chaim Prilusky; lsprilus at bioinformtics.weizmann.ac.il
Status   : Tested (30 Sep 1992).


Organiz. : 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
           readseq sequence reformating program
Contact  : Don Gilbert; gilbertd at cricket.bio.indiana.edu 


Organiz. : 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 at theory.bchs.uh.edu
Status   : Tested (30 Oct 1992).


Organiz. : 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 at genes.nig.ac.jp
Status   : Tested (5 Oct 1992).


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

-------------------------------------------------------------------------------
Organiz.: National Center for Biotechnology Information (NCBI) / USA
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=Multiple sequence alignment program;
          OS=DOS/Windows     
          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
          Name=Authorin; Desc=Program for preparing sequence data for
          submission to the nucleic acid and protein data banks;
          OS=Mac and DOS;
          Directory= /pub/authorin/mac or /pub/authorin/dos
Contact : Scott Federhen; federhen at ncbi.nlm.nih.gov 
Status  : Tested (13 Dec 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Dept. of Genetics / University of Washington / Seattle / USA
Address : evolution.genetics.washington.edu (128.95.12.41)
Programs: Name=PHYLIP; Desc=Phylogeny inference package;
          Directory= /pub
Contact : Joe Felsenstein; joe at 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 at 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; OS=DOS;
          Directory= /pub/molbio/ramha1
Contact:  David P. Siderovski; siderovski at galen.oci.utoronto.ca
Status  : Tested (18 Jan 1993).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
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 at ccu.umanitoba.ca
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: 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; mcp13936 at ggr.co.uk
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: New Mexico State University / USA
Address : haywire.nmsu.edu (128.123.001.032)
Programs: Name=gm; Desc=Gene modeler software package; OS=Unix;
          Directory= /gm
Contact : Chris Fields; cfields at nmsu.edu
Status  : Tested (1 Oct 1992).
------------------------------------------------------------------------------

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

------------------------------------------------------------------------------
Organiz.: University of Virginia / USA
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 at virginia.edu
Status  : Tested (30 Sep 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: Department of Molecular Biology / Massachussetts General Hospital /
          Boston / USA
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 at frodo.mgh.harvard.edu
Status  : Tested (30 Sep 1992).
-------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: Harvard/M.I.T. Division of Health Sciences and Technology and the
          Harvard Division on Aging / Boston / USA
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 at astro.bih.harvard.edu
Status  : Tested (27 Oct 1992).
-------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: University of Illinois / Urbana-Champaign / USA
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 at ncsa.uiuc.edu
Status  : Tested (2 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Mathematics / Stanford University / USA
Address : gnomic.stanford.edu (36.120.0.19)
Programs: Name=SAPS; Desc=Statistical analysis of protein sequences; OS=Unix;
          Directory= /pub
Contact : Volker Brendel; volker at gnomic.stanford.edu
Status  : Tested (2 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Biochemistry / Stanford University / USA
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 at cmgm.stanford.edu
Status  : Tested (29 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Molecular Biology Computer Research Resource (MBCRR) / Boston / USA
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 at mbcrr.harvard.edu 
Status  : Tested (1 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: New England BioLabs (NEB) / USA
Address : vent.neb.com (192.138.220.2)
Programs: Name=detect; Desc=Program that locates errors in DNA sequences;
          OS=UNIX or other OS (source code in C provided);
          Directory= /pub/detect
Contact : Rich Roberts; roberts at neb.com
Status  : Tested (1 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: 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 at ento.csiro.au
Status  : Tested (27 Oct 1992).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Pennsylvania State University / USA
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
Contact : ?
Status  : Tested (30 Oct 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: Rice University / Houston / USA
Address : ion.rice.edu (128.42.70.6)
Programs: Name=MolViewer; Desc=Molecule viewing program; OS=Next UNIX;
          Directory= /pub
Contact : Steve Ludtke; steve at ion.rice.edu
Status  : Tested (2 Feb 1993).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Organiz.: Protein Science
Address : ftp.uci.edu (128.200.80.20)
Programs: Name=Kinemage; OS=Mac or DOS;
          Directory= /protein
Status  : Tested (17 March 1993).
------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Biochemistry and Molecular Biophysics /
          Columbia University / USA
Address : cuhhca.hhmi.columbia.edu (128.59.98.1)
Programs: Name=PDBviewer; Desc=Rendering tool for protein structures as found
          in the PDB; OS=Unix;
          Directory= /pub/programs/PDBview
          Name=WPDB; Desc=Macromolecular Structure Interrogation;
          OS=DOS/Windows
          Directory= /pub/programs/WPDB
Contact : Phil Bourne; system at cuhhca.hhmi.columbia.edu
Status  : Tested (22 March 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Institut fur Theoretische Chemie / Universitat Wien / Austria
Address : ftp.itc.univie.ac.at (131.130.29.27)
Programs: Name=Vienna RNA Package; Desc=Software for folding and comparing
          RNA secondary structures; OS=Unix;
          Directory= /pub/RNA
Contact : Ivo Hofacker; ivo.hofacker at itc.univie.ac.at
Status  : Tested (26 May 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Science and Engineering Research Council / Daresbury Laboratory / UK
Address : ccp4.dl.ac.uk (148.79.160.77)
Programs: CCP4; Descr=Program suite for protein crystallography;
          OS=VMS or Unix;
          Directory= /pub/ccp4
Contact : Secretary to CCP4, SERC Daresbury Laboratory, Warrington WA4 4AD,
          UK; ccp4 at daresbury.ac.uk.
Status  : Tested (5 Aug 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Biochemistry / University of Antwerp (UIA) / Belgium
Address : uiam3.uia.ac.be (143.169.8.1)
Programs: DCSE; Desc=Dedicated Comparative Sequence Editor;
          OS=VMS, Unix or DOS;
          Directory= [.dcse]
Contact : Peter De Rijk; derijkp at reks.uia.ac.be
Status  : Tested (9 Dec 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Medical Genetics / University of British Columbia /
          Canada
Address : ulam.generes.ca (137.82.64.150)
Programs: SAR2RIS; Desc=Convert SeqAnalRef to RIS format; OS=DOS;
          SORFIND; Desc=Exon detection program; OS=DOS;
          Directory= /pub
Contact : Gord Hutchinson; hutch at ulam.generes.ca
Status  : Tested (9 Dec 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Department of Software Engineering (ZXA/US) / BASF Inc /
          Ludwigshafen / Germany
Address : ftp.uni-kl.de (131.246.9.95)
Programs: BIOSIM; Desc=Biologically oriented neural network simulator;
          OS=UNIX or DOS/Windows;
          Directory= /pub/bio/neurobio
Contact : Stefan Bergdoll; bergdoll at zxa.basf-ag.de
Status  : Tested (9 Dec 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Departments of Genetics and Computer and Information Science /
          Computational Biology and Informatics Laboratory /
          Human Genome Project / University of Pennsylvania / USA
Address : cbil.humgen.upenn.edu (130.91.180.83)
Programs: DNA WorkBench; Desc=A program for sequence searching and
          manipulation; OS=UNIX, DOS or Mac;
          Directory= /pub/dnaworkbench
Contact : James Tisdall; tisdall at cbil.humgen.upenn.edu
Status  : Tested (13 Dec 1993).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: ?
Address : nemo.life.uiuc.edu (128.174.183.6)
Programs: Oligo; Desc=Program for choosing optimal oligonucleotides for
          filter hybridization, sequencing and in vitro amplification of DNA;
          Directory= /lim/uploads
Contact : Clark Duncan; duncan at genesys.demon.co.uk
Status  : Tested (1 Feb 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Oak Ridge National Laboratory / USA
Address : arthur.epm.ornl.gov (128.219.9.76)
Programs: XGRAIL; Desc=Client-server implementation of the GRAIL analysis
          tools; OS=UNIX or VMS;
          Directory= /pub/xgrail
Contact : grailmail at ornl.gov
Status  : Tested (1 Feb 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: University of New Hampshire / USA
Address : farfetch.unh.edu (132.177.128.85)
Programs: FARFETCH; Desc=Sequence retrieval client; OS=ALL;
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Laboratory of Molecular Biophysics / University of Oxford / UK
Address : geoff.biop.ox.ac.uk (163.1.16.4)
Programs: Alscript; Desc=Program to take a multiple protein sequence
          alignment and "prettify" it; OS=Unix, VMS and DOS;
          Amps; Desc=Multiple protein sequence alignment and flexible pattern
          matching programs; OS=Unix;
          Amas; Desc=Automatic analysis of multiple protein sequence
          alignments; OS=Unix or VMS;
          Scanps; Desc=Search protein sequence databases with a query
          sequence or multiple alignment; OS=Unix;
          Stamp; Desc=Alignment of multiple protein structures; OS=Unix;
          Assp; Desc=Takes a multiple sequence alignment and estimates the
          lower limit in accuracy one should expect for a perfect consensus
          secondary structure prediction based on the alignment; OS=Unix;
Contact : Geoff. Barton; gjb at bioch.ox.ac.uk
Status  : Tested (1 Feb 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: BioMolecular Structure Group / Glaxo Research and Development /
          Greenford / Middlesex / UK
Address : ftp.dcs.ed.ac.uk (129.215.160.5)
Programs: RasMol; Desc=Molecular graphics visualisation tool;
          OS=UNIX; VMS/DecWindows or DOS/Windows;
          Directory= /pub/rasmol
Contact : Roger Sayle; ras32425 at ggr.co.uk
Status  : Tested (11 March 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Dept. of Biochemistry and Molecular Biology / University College /
          London / UK
Address : ftp.biochem.ucl.ac.uk (128.40.46.11)
Programs: MEMSAT; Desc=Transmembrane structure prediction program; OS=DOS;
          Directory= /pub/MEMSAT
Contact : David Jones; jones at bioc.bsm.ucl.ac.uk
Status  : Tested (6 April 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Organelle Genome Megasequencing Project (OGMP) / Departement de
          Biochimie / Universite de Montreal / Canada
Address : megasun.bch.umontreal.ca (132.204.84.77)
Programs: Clever; Desc=Program for command line access to the Entrez databases;
          OS=Unix, VMS, DOS or Mac;
          Directory= /pub/clever
Contact : ogmp at bch.umontreal.ca
Status  : Tested (1 Feb 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Institut de Biologie et Chimie des Proteines /  Universite Claude
          Bernard Lyon 1 / Lyon / France
Address : ibcp.fr (193.51.160.1)
Programs: SOPM; Desc=Self Optimized Prediction Method (SOPM) is a package to
          make secondary structure predictions of proteins;
          OS=Unix;
Contact : Gilbert Delage; deleage at ibcp.fr
Status  : Tested (2 March 1994).
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: TIMC (URA D1618) / CERMO / Grenoble / France
Address : brise.imag.fr (129.88.110.7)
Programs: Foldit (light); Desc=Molecular modelling program to visualize and
          manipulate proteins; OS=Mac;
          Directory= /pub/mac/programs
Contact : jean-claude.jesior at imag.fr
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Organiz.: Italian EMBNet node / Bari / Italy
Address : ftp.ba.cnr.it (192.195.110.132)
Programs: WORDUP; Desc=Dynamically detect significant signals of any length
          in a DNA sequence; OS=VMS;
          Directory= pub/software/wordup
Contact : Sabino Liuni; liuni at mvx36.csata.it                                                  ~
Status  : Tested (18 April 1994).
-------------------------------------------------------------------------------

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



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