List of molecular biology Email servers / Release 1.50

Amos Bairoch BAIROCH at cmu.unige.ch
Mon Aug 2 16:22:31 EST 1993


==============================================================================
Name   : serv_ema.txt
Version: 1.50 / July 30, 1993
Concern: List of molecular biology email servers
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 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 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) MAILFASTA
  -------------

MAILFASTA is a UNIX shell script which will take a DNA or PROTEIN sequence
and will reformat it and mail it to any  or  all  of  the following  email
servers  (which  are  all described  in  section B below):  BLAST,  BLITZ,
BLOCKS, FASTA, Geneid, GRAIL, PredictProtein, and Pythia.

MAILFASTA is  a  public  domain  program  developed by Thon de Boer of the
Department of Microbiological  Physiology  at  the  Vrije universiteit  in
Amsterdam Holland. He can be contacted at: deboer at bio.vu.nl

The current version of the program is: 3.2 of July 1993

The program can be downloaded from various ftp sites such as at EMBL (ftp.
embl-heidelberg.de)  or at the iubio archive site (iubio.bio.indiana.edu).
And its  can  also be obtained  by email from the EMBL Network File Server
(see the description in section B below).

MAILFASTA is packed as an shell archive. It contains :

mailfasta         : The UNIX shell script
cid.c             : A small c program which will determine if the sequence
                    is DNA or protein.
getentry          : A shell script  which  can be used to retrieve entries
                    of interest
mailfasta.doc     : The documentation file
mailfasta.changes : A file stating the changes since version 2.1
 
Warning: MAILFASTA makes use of the program 'readseq' for file conversion.
This program  MUST  be present and is NOT included with the shell archive,
you must also get it by ftp or by email.


  A4) Acknowledgments
  -------------------

Many thanks  to  all  those  who  provided  me  information that was used  in 
compiling this file, especially  to Bob Harper (harper at convex.csc.fi) and Tan
Tin Wee (bchtantw at nuscc.nus.sg) who  forwarded  or  provided  me with lots of
information.


  A5) Additional references
  -------------------------

A very good summary of  what you can do with electonic mail  servers has been
recently published:

Henikoff S.
Sequence analysis by electronic mail server.
Trends Biochem. Sci. 18:267-268(1993).


  A6) Release history
  -------------------

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

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

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Entry      : EMS0025
Name       : BIOSCI waismail server
Organiz.   : BIOSCI / IntelliGenetics Inc / Mountain View / USA
Type       : RETRIEVAL
Description: This server can be used for text searching of the following two
             BIOSCI WAIS archives: biosci (complete archive of BIOSCI/bionet
             postings) and biology-journal-contents (archive of BIO-JOURNAL/
             bionet.journals.contents table of contents postings).
Address    : waismail at net.bio.net
Contact    : To report problems: biosci at net.bio.net
Status     : Tested (11 May 1993).
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//
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Entry      : EMS0001
Name       : BIOSERVE
Organiz.   : Group T-10 / Los Alamos National Laboratory / USA
Type       : RETRIEVAL
Description: Allows the retrieval of: documents  concerning  GenBank (feature
             table, flatfile format,  submission form,  transaction protocol,
             etc.); the LimB database; a number of  software packages (alpar,
             alwin, score, signal-scan, trna-scan, etc.).  You  can  also use
             this server to retrieve a  GenBank entry  or  to be aware of any
             overlap in sequencing  effort  with  other  investigators (cdna-
             inform).
Address    : bioserve at temin.lanl.gov
Contact    : To report problems: michael at genome.lanl.gov
Status     : Tested (15 Jan 1993).
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//
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Entry      : EMS0002
Name       : BLAST e-mail server
Organiz.   : 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 searches.
Address    : blast at ncbi.nlm.nih.gov
Contact    : To report problems: blast-help at ncbi.nlm.nih.gov
Status     : Tested (30 Dec 1992).
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//
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Entry      : EMS0014
Name       : BLITZ electronic mail server (MPsrch)
Organiz.   : Edinburgh University Biocomputing Research Unit (BRU) / U.K. and
             European Molecular Biology Laboratory / Heidelberg / Germany
Type       : ANALYSIS
Description: Email server for the MPsrch program from the BRU.  MPsrch allows
             you to perform sensitive and extremely fast  comparisons of your
             protein sequences  against  the  Swiss-Prot  database  using the
             Smith and Waterman best local similarity algorithm.  Runs on the
             MasPar family  of  massively parallel machines.  MPsrch  is  the
             fastest implementation of  the  SW algorithm currently available
             on any machine.  
Address    : blitz at embl-heidelberg.de
Contact    : To report problems: nethelp at embl-heidelberg.de
Status     : Tested (29 Jul 1993).
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//
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Name       : BLOCKS e-mail searcher
Organiz.   : Fred Hutchinson Center / Seattle / USA
Type       : ANALYSIS and RETRIEVAL
Description: Compares a protein or DNA  sequence  to  the current database of
             protein blocks.  Blocks  are  short  multiply  aligned  ungapped
             segments corresponding to the  most  highly conserved regions of
             proteins. The BLOCKS database has been constructed by successive
             application  of  the  automated PROTOMAT  system  to  individual
             entries  in the PROSITE catalog of  protein  groups keyed to the
             SWISS-PROT protein sequence database.
             You can  also  use  this server to retrieve specifics blocks and
             PROSITE entries.
Address    : blocks at howard.fhcrc.org
Contact    : To report problems: jorja at sparky.fhcrc.org
Status     : Tested (3 Jan 1993).
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//
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Entry      : EMS0003
Name       : DAPMAIL
Organiz.   : 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 at ed.ac.uk
Status     : Tested (30 Dec 1992).
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//
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Entry      : EMS0004
Name       : Darwin
Organiz.   : 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 a


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