internet for the mol. biologist

Francis Ouellette francis at borduas.nlm.nih.gov
Wed Oct 26 10:19:27 EST 1994


And here is the list of Email server ... also of great
interest to net-minded molecular biologists

regards,

francis

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


==============================================================================
Name   : serv_ema.txt
Version: 3.00 / September 23, 1994
Concern: List of molecular biology email servers
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 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 EBI (ftp.
ebi.ac.uk) or at the iubio archive site (iubio.bio.indiana.edu). And it can
also be  obtained   by  email from the  EBI  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) MSU (Mail Server Utility)
  -----------------------------

MSU is  a    program,  written in  ANSI C,  that  facilitates the use of email
sequence analysis  servers.  It  reformats  nucleotide  and protein sequences,
lets users  choose  from  a menu of services and helps them to submit a proper
service requests.  By using an external control file for defining services and
menus, it  is highly flexible and can be easily extended and customised with a
simple text editor.  At  present  it  allows access to 22 email-based sequence
analysis services.

MSU is developed by Rainer Fuchs  from Glaxo Research Institute (USA).  He can
be contacted at: rf11522 at glaxo.com

The current version of the program is: 1.3 of March 1994

The program    is    freely    available    and   can   be   downloaded   from
ftp.ebi.ac.uk (UNIX  version:  /pub/software/unix/msu.tar.Z;  OpenVMS version:
/pub/software/vax/msu.uue).  It  can  also  be  obtained by email from the EBI
Network File Server (see description in section B below).

Citation: 

Fuchs R.
Sequence analysis by electronic mail: a tool for accessing internet e-mail
servers.
Comput. Appl. Biosci. 10:413-417(1994).


  A5) 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.


  A6) Additional references
  -------------------------

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

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


  A7) 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) LIST OF EMAIL SERVERS
------------------------

Total number of servers listed: 44

------------------------------------------------------------------------------
Entry      : EMS0034
Name       : Bicserv
Organiz.   : EMBNet Israeli National Node / Biological Computing Devision /
             Weizmann Institute of Science / Israel
Type       : ANALYSIS
Description: Allows users to send a nucleotide or protein query  sequence  to
             the BIOCCELERATOR server (which use a  special-purpose  hardware
             accelerator) to do either a Smith-Waterman database searche or a
             Gribskov et al. profile search as implemented in the GCG package
Address    : bicserv at sgbcd.weizmann.ac.il
Contact    : To report problems: lsestern at weizmann.weizmann.ac.il
Status     : Tested (28 Feb 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0043
Name       : Biosafety
Organiz.   : International Centre for Genetic Engineering and Biotechnology
             (ICGEB) / Trieste / Italy
Type       : RETRIEVAL
Description: Retrieval of documents that  covers  various  safety  aspects of
             biotechnology,  especially:  laboratory  chemical and biosafety;
             use and release of genetically modified organisms;  biodiversity
             issues pertinent to biotechnology.
Address    : docserver at icgeb.trieste.it
Contact    : To report problems: docserver-comment at icgeb.trieste.it
Status     : Tested (28 July 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0029
Name       : BioSCAN
Organiz.   : Department of Computer Science / University of North Carolina
             Chapel Hill / USA
Type       : ANALYSIS
Description: Allows users to send a nucleotide or protein query  sequence  to
             the   BioSCAN  server  (which  use  a  special-purpose  hardware
             accelerator) to do a similarity search with an algorithm similar
             to BLAST. The search can be done on SWISS-PROT, PIR, or GenBank.
Address    : bioscan at cs.unc.edu
Contact    : To report problems: bioscan-info at cs.unc.edu
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0025
Name       : BIOSCI waismail server
Organiz.   : BIOSCI / IntelliGenetics Inc / Mountain View / California / USA
Type       : RETRIEVAL
Description: This  server  can  be  used  for  text searching of the following 
             three BIOSCI WAIS archives: biosci (complete  archive  of BIOSCI/
             bionet postings);   biology-journal-contents   (archive of BIOSCI
             table of contents postings); and Biologists-addresses.
Address    : waismail at net.bio.net
Contact    : To report problems: biosci-help at net.bio.net
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
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 (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
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 (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0014
Name       : BLITZ electronic mail server (MPsrch)
Organiz.   : Edinburgh University Biocomputing Research Unit (BRU) / UK and
             European Bioinformatics Institute / Hinxton / UK
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 ebi.ac.uk
Contact    : To report problems: nethelp at ebi.ac.uk
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0041
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: henikoff at howard.fhcrc.org
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0003
Name       : DAPMAIL
Organiz.   : Edinburgh University Biocomputing Research Unit (BRU) / UK
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 (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
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 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 at inf.ethz.ch
Contact    : To report problems: knecht at inf.ethz.ch
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0027
Name       : dFLASH server
Organiz.   : IBM Research Division's Thomas J. Watson Research Center /
             Yorktown Heights / USA
Type       : ANALYSIS
Description: "Homologous sequence retrieval"   program   for  protein and DNA
             sequences based  on  the  FLASH algorithm (Fast-Lookup Algorithm
             for Sequence Homology). Currently operates with PIR and GenBank.
Address    : dflash at watson.ibm.com
Contact    : To report problems: dflash at watson.ibm.com; the "Subject" line
             should contain the word "comments".
Note       : To get help send a message with the word "dFLASH" in the
             "Subject" line a body containing the words "send help".
Status     : Tested (28 Jul 1993).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0038
Name       : DOMAIN
Organiz.   : Agricultural Biotechnology Center / Godollo / Hungary
Type       : ANALYSIS
Description: Will do a search  (using Blast)   of  a protein sequence against
             SWISS-PROT and  will  report a list of the  most frequent domain
             homologies.
Address    : domain at hubi.abc.hu
Contact    : To report problems: domain-comment at hubi.abc.hu
Status     : Tested (7 April 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0005
Name       : EBI Network File Server
Organiz.   : European Bioinformatics Institute / Hinxton / UK
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  EBI anonymous FTP server is
             described in the "serv_ftp.txt" file.
Address    : netserv at ebi.ac.uk
Contact    : To report problems: nethelp at ebi.ac.uk
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0006
Name       : EBI Mail-FASTA Server
Organiz.   : European Bioinformatics Institute / Hinxton / UK
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.  The EMBL
             database is updated daily.
             [The purpose and use of this server is identical  to that of the
             GENIUSnet Mail-Fasta Service (entry EMS0010)]
Address    : fasta at ebi.ac.uk
Contact    : To report problems: nethelp at ebi.ac.uk
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0040
Name       : EBI Mail-PROSITE Server
Organiz.   : European Bioinformatics Institute / Hinxton / UK
Type       : ANALYSIS
Description: Allows to rapidly compare  your new protein sequence against all
             patterns stored in the PROSITE pattern database. 
Address    : prosite at ebi.ac.uk
Contact    : To report problems: nethelp at ebi.ac.uk
Status     : Tested (7 May 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0007
Name       : EST Report Mail Server
Organiz.   : National Center for Biotechnology Information /
             National Library of Medicine / NIH / Bethesda / USA
Type       : RETRIEVAL
Description: Allows the retrieval of  Expressed Sequence Tag  (EST) sequences
             from the dbEST collection. You  can  request  ESTs by specifying
             either their NCBI id or their GenBank AC numbers, GDB ids, etc.
Address    : est_report at ncbi.nlm.nih.gov
Contact    : To report problems: carolyn at ncbi.nlm.nih.gov
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0008
Name       : Flat DB E-Mail Network Server
Organiz.   : 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 at smlab.eg.gunma-u.ac.jp
Contact    : To report problems: smiyazaw at smlab.eg.gunma-u.ac.jp
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0039
Name       : GCRDb Email Fasta Search Server
Organiz.   : Massachusetts General Hospital / Charlestown / USA
Type       : ANALYSIS
Description: Will do a search (using Fasta) of a protein sequence against the
             most current  version  of  GCRDb (the G-protein-coupled receptor
             database).
Address    : gcrdb at receptor.mgh.harvard.edu
Contact    : To report problems: lfk at receptor.mgh.harvard.edu
Status     : Tested (7 April 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0033
Name       : GDB/OMIM mail server
Organiz.   : Johns Hopkins University School of Medicine / Baltimore /
             Maryland / USA
Type       : RETRIEVAL
Description: Allows to retrieve documents from GDB or OMIM through simple
             keyword searches.
Address    : mailserv at gdb.org
Contact    : To report problems: help at gdb.org
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0044
Name       : Genefinder
Organiz.   : Baylor College of Medicine Computational Biology Group / Houston
             USA
Type       : ANALYSIS
Description: Offers five different services:
             FGENEH: prediction of gene structure in human DNA sequences
             FEXH  : prediction of internal 5' and 3' exons in human DNA
                     sequences
             HEXON : prediction of internal exons in human DNA sequences
             HSPL  : splice site prediction in human DNA sequences
             SSP   : prediction of alpha-helix and beta-strand segments of
                     globular proteins
Address    : service at theory.bchs.uh.edu
Note       : Each of the individual services listed above is accessed by
             using the name of the service in the subject line of the message.
Contact    : To report problems: solovyev at cmb.bcm.tmc.edu
Status     : Not yet tested.
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0009
Name       : Geneid
Organiz.   : 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 at bir.cedb.uwf.edu
Contact    : To report problems: steen at bir.cedb.uwf.edu.
Note       : To get help send "geneid info" instead of "help".
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0010
Name       : GENIUSnet Mail-Fasta Service 
Organiz.   : German Cancer Research Centre (DKFZ) / 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.
             [The purpose and use of this server is identical  to that of the
             the EBI Mail-FASTA Server (entry EMS0006)]
Address    : mfasta at genius.embnet.dkfz-heidelberg.de
Contact    : To report problems: dok419 at genius.embnet.dkfz-heidelberg.de
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0011
Name       : GENIUSnet sequence-server
Organiz.   : German Cancer Research Centre (DKFZ) / Heidelberg / Germany
Type       : RETRIEVAL
Description: Allows to  retrieve entries  from  the EMBL, GenBank, SWISS-PROT
             and PIR sequence  databases using either the entry name  or  the
             accession number. The sequences returned are in the GCG format.
Address    : netserv at genius.embnet.dkfz-heidelberg.de
Contact    : To report problems: dok419 at genius.embnet.dkfz-heidelberg.de
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0012
Name       : GenMark
Organiz.   : Georgia Tech School of Applied Biology and Office of Information
             Technology / Atlanta / USA
Type       : ANALYSIS
Description: System  for  predicting  protein  coding  regions in 10 prokaryotic             and 11 eukaryotic species (including mammals, plants,
             bacteria etc.) It is based on a special type of Markov chain model
             of coding and noncoding nucleotide sequences as described in 
             Computers & Chemistry (1993), v.17(2), 122-133.
             As an option translated sequences from predicted gene regions can  
             be immediately tested for sequence similarity by BLAST program.  
Address    : genmark at ford.gatech.edu
Contact    : To report problems: mb56 at prism.gatech.edu
                             or: gt1619a at prism.gatech.edu
Status     : Tested (25 July 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0032
Name       : GenQuest (Q) (Sequence Comparison System)
Organiz.   : Oak Ridge National Laboratory / USA
Type       : ANALYSIS
Description: Allows rapid and sensitive comparison of DNA and protein sequence
             to existing DNA  and  protein sequence  databases.  The databases
             which can be  accessed  from  the Q  server  include  the  Genome
             Sequence Database (GSDB); SWISS-PROT, Prosite, PDB and RepBase.
Address    : q at ornl.gov  
Contact    : To report problems: grailmail at ornl.gov  
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0013
Name       : GRAIL (Gene Recognition and Analysis Internet Link)
Organiz.   : Oak Ridge National Laboratory / USA
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 at ornl.gov
Contact    : To report problems: grailmail at ornl.gov
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0037
Name       : HUGEMAP
Organiz.   : CEPH-Genethon / Paris / France
Type       : RETRIEVAL
Description: Allows to access  Genethon's human physical map  data on clones,
             YACs or STSs.
Address    : hugemap at genethon.fr
Contact    : To report problems: hugemap at genethon.fr
             Note: put 'message' or 'hugemap' as the subject in your mail.
Status     : Tested (11 Mar 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0041
Name       : MOTIF E-Mail Server on GenomeNet
Organiz.   : Supercomputer Laboratory / Institute for Chemical Research / Kyoto /
             Japan
Type       : ANALYSIS
Description: Allows to rapidly compare  your new protein sequence against all
             patterns stored in  the PROSITE pattern  database as well as the  
             MotifDic library.
Address    : motif at genome.ad.jp
Contact    : To report problems: motif-manager at genome.ad.jp
Status     : Tested (13 May 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0028
Name       : MOWSE
Organiz.   : Imperial Cancer Research Fund and SERC Daresbury Laboratory / UK
Type       : ANALYSIS
Description: Peptide mass fingerprint  email server service. MOWSE allows the
             identification of known proteins from a set of molecular weights
             (mass spec) determined after proteolytic digests.
Address    : mowse at dl.ac.uk
Contact    : To report problems: mbdpn at s-crim1.dl.ac.uk
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0015
Name       : NetGene mail server
Organiz.   : Department of Physical Chemistry / Technical University of
             Denmark / Lyngby / Denmark 
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 at virus.fki.dth.dk
Contact    : To report problems: engel at virus.fki.dth.dk
Status     : Tested (30 Dec 1992).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0030
Name       : nnpredict
Organiz.   : University of California - San Francisco (UCSF) / USA
Type       : ANALYSIS
Description: Analyze a protein sequence and  sends  back  a prediction of the
             secondary  structure  using  a  two-layer,  feed-forward  neural
             network method.
Address    : nnpredict at celeste.ucsf.edu
Contact    : To report problems: nnpredict-request at celeste.ucsf.edu
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0016
Name       : PDB e-mail file server
Organiz.   : Protein Data Bank / Brookhaven National Laboratory / USA
Type       : RETRIEVAL
Description: Provides PDB general information and documentation files.
Address    : fileserv at 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 at bnl.gov
Status     : Tested (7 Jan 1993).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0017
Name       : PredictProtein
Organiz.   : Protein Design Group / European Molecular Biology 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 at embl-heidelberg.de
Contact    : To report problems: predict-help at embl-heidelberg.de
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
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Entry      : EMS0018
Name       : PIR Network Request Service
Organiz.   : Protein Information 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, NRL_3D, PATCHX, GenBank and EMBL.
             You  can also use it for FASTA searches of protein or nucleotide
             sequences (which  will be translated in its six  reading frames)
             against the PIR, NRL_3D, and PATCHX databases.
Address    : fileserv at nbrf.georgetown.edu
Contact    : To report problems: postmaster at nbrf.georgetown.edu
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
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Entry      : EMS0036
Name       : Prodom
Organiz.   : INRA Toulouse / France
Type       : RETRIEVAL and ANALYSIS
Description: Allows to querying the  protein  domain  database ProDom for the
             domain organization of a known protein stored in SWISS-PROT. 
             Allows to fetching domain families and their consensus sequences
             Allows to searching ProDom with BLAST.
Address    : prodom at toulouse.inra.fr
Contact    : To report problems: proquest at toulouse.inra.fr.
Status     : Tested (2 March 1994).
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//
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Entry      : EMS0019
Name       : Pythia
Organiz.   : 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. Can also be used to identify the presence
             of Alu sequences and to classify them into subfamilies.
Address    : pythia at anl.gov
Contact    : To report problems: pythia-admin at anl.gov
Status     : Tested (30 Dec 1992).
------------------------------------------------------------------------------
//
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Entry      : EMS0020
Name       : EBI Mail-QUICKSEARCH server
Organiz.   : European Bioinformatics Institute / Hinxton / UK
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) ?  The databases are updated daily.
Address    : quick at ebi.ac.uk
Contact    : To report problems: nethelp at ebi.ac.uk
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0026
Name       : RDP mail server
Organiz.   : Ribosomal Database Project / University of Illinois / Urbana /
             Illinois / USA
Type       : RETRIEVAL
Description: Access to data and software relative to ribosomal RNA sequences.
Address    : server at rdp.life.uiuc.edu
Contact    : To report problems: rdp at phylo.life.uiuc.edu
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
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Entry      : EMS0021
Name       : RETRIEVE E-Mail Server
Organiz.   : 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, EPD, PDB, etc.
Address    : retrieve at ncbi.nlm.nih.gov
Contact    : To report problems: retrieve-help at ncbi.nlm.nih.gov
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0031
Name       : SBASE
Organiz.   : International Centre for Genetic Engineering and Biotechnology
             (ICGEB) / Trieste / Italy
Type       : ANALYSIS
Description: Will do a search (using Blast) of a protein sequence against the
             SBASE database of protein sequence domains.
Address    : sbase at icgeb.trieste.it
Contact    : To report problems: sbase-comment at icgeb.trieste.it
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0035
Name       : SOPM
Organiz.   : Institut de Biologie et Chimie des Proteines /  Universite Claude
             Bernard Lyon 1 / Lyon / France
Type       : ANALYSIS
Description: Will analyse a protein  sequence  with  the SOPM (Self Optimized
             Prediction   Method)   package  to   make   secondary  structure
             predictions of proteins.
Address    : deleage at ibcp.fr
Contact    : To report problems: deleage at ibcp.fr
Status     : Tested (Not yet).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0023
Name       : Springer Journals Preview Service
Organiz.   : Springer Verlag, Dept. New Technologies / Berlin / Germany
Type       : RETRIEVAL
Description: Distribution of the table of contents and abstracts for selected
             life sciences  journals published by Springer Verlag.  The table
             of contents are free,  but there is a charge of 20$ per year for
             the abstracts of 30 journals.
Address    : svjps at vax.ntp.springer.de
Contact    : To report problems: springer at vax.ntp.springer.de
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0024
Name       : TM7 file server
Organiz.   : Protein Design Group / European Molecular Biology Laboratory
             (EMBL) / Heidelberg / Germany
Type       : RETRIEVAL
Description: Holds  data and  programs related to G-protein coupled receptors
             that possess the seven helix transmembrane bundle motif.
Address    : tm7 at embl-heidelberg.de
Contact    : To report problems: vriend at embl-heidelberg.de
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
------------------------------------------------------------------------------
Entry      : EMS0022
Name       : University of Houston Gene-Server
Organiz.   : University of Houston / Houston / USA
Type       : RETRIEVAL
Description: Allows to retrieve  entries  from  the GenBank  and PIR sequence
             databases using various text search parameters.  It  also allows
             the retrieval of public  domain  software  for MS-DOS computers,
             the Apple Macintosh, DEC VAX/VMS, and UNIX as well as additional
             text files such as the BIO-Matrix newsletters.
Address    : gene-server at bchs.uh.edu
Contact    : To report problems: gene-server-management at evolution.bchs.uh.edu
Status     : Tested (26 Jan 1994).
------------------------------------------------------------------------------
//
=End=of=document==============================================================




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