From: BAIROCH@cmu.unige.ch (Amos Bairoch)
Newsgroups: bionet.announce
Subject: List of molecular biology email servers (Preliminary edition).
Date: 7 Jan 93 01:29:29 GMT


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Name   : serv_ema.txt
Version: 0.9 / January 6, 1993
Concern: List of molecular biology email servers
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
         bairoch@cmu.unige.ch
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    THIS IS A PRELIMINARY VERSION OF THIS DOCUMENT, FEEDBACK IN THE FORM
            OF CORRECTIONS, ADDITIONS, ETC ARE MORE THAN WELCOME !!! 
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A) INTRODUCTION
===============

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

This document briefly describes the various email servers that are available
to molecular biologists. The servers  described  in  this document generally
fall into one of the following two categories:

    1) Servers that provide an analytical function.  You  need to provide to
       such a server nucleic acid or a protein sequence(s), the server sends
       back the  result  of  an  analysis  (for example a similarity search)
       carried out on the sequences(s).

    2) Servers that allow you to retrieve all or part of a database.

Note that some servers can fall into both categories.

We do not describe here the sites that allows the transfer  of files by what
is known as anonymous "ftp" (File transfer protocol), nor do we describe the
BIOSCI electronic newsgroup system or  the other bulletin  boards  that  are
available  to  molecular biologist.  These  services  are  described  in the
following documents:

   serv_ftp.txt: For a list of molecular biology FTP servers for databases
                 and software.
   serv_bbo.txt: For a list of bulletin boards services for molecular
                 biologists.


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

1) Except when noted otherwise all  the  servers listed in this document will
   send you a full description of the  service that they offer and the syntax
   that they support if you send a message containing only the word:

              help

   to the correct email address of the server.

   As the services offered by most of these servers generally  evolve and get
   expanded, it is a good idea  to request, every six  months or so, the help
   documentation files of the servers that you are using.


2) Most of these servers provide an email address where you can reach a human
   interlocutor to report problems.  Before you send mail to such an address,
   make sure that the current version of the help documentation file does not
   already provide the answer to your question(s) !!


3) Please be patient !!!   Some of the servers described in this document are
   accessed by many users  and the response time  can vary with the load.  In
   addition network trafic has a  significant impact  on the transit time for
   an email message. So  if  you  have  submitted a  request  to a server you
   should at least wait  48 hours  before  taking  any further step.  At that
   point you should not directly resubmit your request, but send a message to
   the address used to reports problems so as to inquire on the status of the
   server.


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

Release 0.9 / January 6, 1993

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B) LIST OF EMAIL SERVERS
------------------------

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Name       : BLAST e-mail server
Organism   : National Center for Biotechnology Information
             National Library of Medicine / NIH / Bethesda / USA
Type       : ANALYSIS
Description: The BLAST algorithm is a heuristic for finding ungapped, locally
             optimal sequence alignments. The BLAST family of programs employs
             this algorithm to compare an amino acid query sequence against a
             protein sequence database or a nucleotide query sequence against
             a nucleotide sequence database, as well as other combinations of
             protein and nucleic acid.
Address    : blast@ncbi.nlm.nih.gov
Contact    : To report problems: blast-help@ncbi.nlm.nih.gov
Status     : Tested (30 Dec 1992).
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Name       : DAPMAIL
Organism   : Edinburgh University Biocomputing Research Unit (BRU) / U.K.
Type       : ANALYSIS
Description: Fast sequence database searching programs that runs on an Active
             Memory Technology Distributed Array Processor AMT DAP.
Address    : dapmail@ed.ac.uk
Status     : Tested (30 Dec 1992).
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Name       : Darwin
Organism   : Computational Biochemistry Research Group (CBRG)
             ETH / Zurich / Switzerland
Type       : ANALYSIS
Description: Give access to various analytical functions implemented in the 
             Darwin sequence analysis package; such as:
             PepPepSearch: search a protein sequence against the SWISS-PROT
             database using Smith-Waterman's version of dynamic programming.
             NuclPepSearch: search a nucleotide sequence directly against the
             entire SWISS-PROT database using the algorithm by Knecht and
             Gonnet.
             PepNuclSearch: search a protein sequence directly against the
             entire EMBL nucleotide database using the algorithm by Knecht
             and Gonnet.
             MassSearch: search the SWISS-PROT database for sequences which
             when digested by the given enzyme will match the given set of
             weights.
Address    : cbrg@inf.ethz.ch
Contact    : To report problems: knecht@inf.ethz.ch
Status     : Tested (30 Dec 1992).
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Name       : EMBL Network File Server
Organism   : European Biology Molecular Laboratory (EMBL)
             Heidelberg / Germany
Type       : RETRIEVAL
Description: This server allows the retrieval via email of EMBL and SWISS-PROT
             entries as well  as a wide variety of databases.  It  also allows
             the retrieval of public domain software for MS-DOS computers, the
             Apple  Macintosh,  DEC  VAX/VMS,  and  UNIX.   The  programs  are
             distributed in a form that is first compressed and then converted
             from binary to a printable ASCII text file.
Note       : You can also obtain all of these  databases  and  software by FTP.
             If you have access to FTP you should  use that method rather than
             use the email  file  server.   The  EMBL  anonymous FTP server is
             described in the "serv_ftp.txt" file.
Address    : netserv@embl-heidelberg.de
Contact    : To report problems: nethelp@embl-heidelberg.de
Status     : Tested (30 Dec 1992).
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Name       : Mail-FASTA
Organism   : European Biology Molecular Laboratory (EMBL)
             Heidelberg / Germany
Type       : ANALYSIS
Description: Allows to perform fast and sensitive comparisons of nucleic acid
             or protein sequences against  various  databases.  Mail-FASTA is
             based on the FASTA program developed by Pearson and Lipman (PNAS
             85:2444-2448(1988)) as implemented in the GCG package.
Address    : fasta@embl-heidelberg.de
Contact    : To report problems: nethelp@embl-heidelberg.de
Status     : Tested (30 Dec 1992).
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Name       : Flat DB E-Mail Network Server
Organism   : Faculty of Technology / Gunma University / Japan 
Type       : RETRIEVAL AND ANALYSIS
Description: Allows to retrieve entries from sequence databases using various 
             text search parameters. This server gives you access to GenBank,
             EMBL, SWISS-PROT, PIR, GenPept, and PRF.
             Give access  to  the  following  analysis  functions:   generate
             complementary strands of DNA sequences; scan databases using the
             various  FASTA   programs  (fasta,  tfasta,  lfasta);   evaluate
             statistical  significance  of  sequence  matching  (RDF2, RDF2G,
             etc.).
Address    : flat-netserv@smlab.eg.gunma-u.ac.jp
Contact    : To report problems: smiyazaw@smlab.eg.gunma-u.ac.jp
Status     : Tested (31 Dec 1992).
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Name       : Geneid
Organism   : Molecular Biology Computer Research Resource (MBCRR)
             Boston / USA
Type       : ANALYSIS
Description: Artificial intelligence system for analyzing vertebrate genomic
             DNA and for the  prediction  of  exons  and  gene  structure as 
             described in J. Mol. Biol. 226:141-157(1992).
Address    : geneid@darwin.bu.edu
Contact    : To report problems: steen@darwin.bu.edu
Note       : To get help send "geneid info" instead of "help".
Status     : Tested (4 Jan 1993).
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Name       : GenMark
Organism   : Georgia Tech School of Applied Biology and Office of Information
             Technology / USA
Type       : ANALYSIS
Description: System  for  predicting  protein  coding  regions in E. coli and
             closely related species. It is based on a special type of Markov
             chain model of coding and noncoding nucleotide sequences.
Address    : genmark@ford.gatech.edu
Contact    : To report problems: mb56@hydra.gatech.edu
Note       : To get help you need to send "instructions" as the subject line
             of your message.
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------------------------------------------------------------------------------
Name       : GRAIL (Gene Recognition and Analysis Internet Link)
Organism   : Oak Ridge National Laboratory
Type       : ANALYSIS
Description: System  for  predicting  protein  coding  regions  in human DNA
             sequences using a neural network approach as described  in PNAS
             88:11261-11265(1991).
Address    : grail@ornl.gov
Contact    : To report problems: grailmail@ornl.gov
Status     : Tested (4 Jan 1993).
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------------------------------------------------------------------------------
Name       : NetGene mail server
Organism   : Department of Physical Chemistry
             Technical University of Denmark
             Lyngby / Denmrk 
Type       : ANALYSIS
Description: Produce neural network predictions of splice sites in vertebrate
             genes as described in J. Mol. Biol. 220:49-65(1991).
Address    : netgene@virus.fki.dth.dk
Contact    : To report problems: engel@virus.fki.dth.dk
Status     : Tested (30 Dec 1992).
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------------------------------------------------------------------------------
Name       : PDB e-mail file server
Organism   : Protein Data Bank / Brookhaven National Laboratory / USA
Type       : RETRIEVAL
Description: Provides PDB general information and documentation files.
Address    : fileserv@pb1.pdb.bnl.gov
Note       : To get help send a message containing the following type of line:
          	               send info your_e-mail_address.
Contact    : To report problems: skora@bnl.gov
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------------------------------------------------------------------------------
Name       : PredictProtein
Organism   : Protein Design Group
             European Biology Molecular Laboratory (EMBL)
             Heidelberg / Germany
Type       : ANALYSIS
Description: Analyze a protein  sequence and  sends  back a multiple sequence
             alignment performed by a  weighted  dynamic  programming  method
             (MaxHom) and  a  secondary structure  prediction  produced  by a
             profile network method (PHD).
Address    : predictprotein@embl-heidelberg.de
Contact    : To report problems: predict-help@embl-heidelberg.de
Status     : Tested (30 Dec 1992).
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Name       : Protein Identification Resource Network Request Service
Organism   : Protein Identification Resource
             National Biomedical Research Foundation
             Washington, DC / USA
Type       : RETRIEVAL AND ANALYSIS
Description: General purpose server that allows the retrieval of entries from
             sequence databases  using various  text  search parameters. This
             server gives you access to PIR, GenBank, and EMBL.  You can also
             use it for a FASTA search of a  protein or a nucleotide sequence
             (which will be translated into  its  six reading frames) against
             the PIR data bank.
Address    : fileserv@gunbrf.bitnet or fileserv@nbrf.georgetown.edu
Contact    : To report problems: postmaster@gunbrf.bitnet
Status     : Tested (4 Jan 1993).
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------------------------------------------------------------------------------
Name       : Pythia
Organism   : Biological and Medical Research Division
             Argonne National Laboratory / Argonne / USA
Type       : ANALYSIS
Description: Allows the identification of human  repetitive  DNA elements such
             as L1, MERx, LTR, etc. Also can be used to identify Alu sequences
             and classify them into subfamilies.
Address    : pythia@anl.gov
Contact    : To report problems: pythia-admin@anl.gov
Status     : Tested (30 Dec 1992).
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------------------------------------------------------------------------------
Name       : Mail-QUICKSEARCH
Organism   : European Biology Molecular Laboratory (EMBL)
             Heidelberg / Germany
Type       : ANALYSIS
Description: Service based on the QUICKSEARCH and QUICKSHOW programs developed
             by J. Devereux as  implemented in the GCG package.   It allows to
             perform very rapid comparisons of a nucleic acid sequence against
             the EMBL and GenBank databases. It  answers  the  question:  does
             this sequence already occur in the database (with  a small number
             of mismatches) ?
Address    : quick@embl-heidelberg.de
Contact    : To report problems: nethelp@embl-heidelberg.de
Status     : Tested (30 Dec 1992).
------------------------------------------------------------------------------

------------------------------------------------------------------------------
Name       : RETRIEVE E-Mail Server
Organism   : National Center for Biotechnology Information
             National Library of Medicine / NIH / Bethesda / USA
Type       : RETRIEVAL
Description: Allows to retrieve entries from sequence databases using various 
             text search parameters. This server gives you access to GenBank,
             EMBL, SWISS-PROT, PIR, GenPept, Kabat, etc.
Address    : retrieve@ncbi.nlm.nih.gov
Contact    : To report problems: retrieve-help@ncbi.nlm.nih.gov
Status     : Tested (30 Dec 1992).
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