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Name : serv_ema.txt
Version: 2.00 / February 1, 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
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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.
pub/BIOSCI/doc/biosci.FAQ. This document may also be requested by e-mail
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) 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.
MSU was developed by Rainer Fuchs from the EMBL Data Library, EMBL Heidelberg,
Germany. He can be contacted at: fuchs at embl-heidelberg.de
The current version of the program is: 1.1 of December 1993
The program is freely available and can be downloaded from
ftp.embl-heidelberg.de (UNIX version: /pub/software/unix/msu.tar.Z; OpenVMS
version: /pub/software/vax/msu.uue). It can also be obtained by email from the
EMBL Network File Server (see description in section B below).
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'), FTP sites ('.ftp') and general
information files ('.txt').
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B) LIST OF EMAIL SERVERS
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Total number of servers listed: 33
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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).
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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 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-help at net.bio.net
Status : Tested (26 Jan 1994).
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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 (26 Jan 1994).
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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 (26 Jan 1994).
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Entry : EMS0014
Name : BLITZ electronic mail server (MPsrch)
Organiz. : Edinburgh University Biocomputing Research Unit (BRU) / UK 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 (26 Jan 1994).
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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: henikoff at howard.fhcrc.org
Status : Tested (26 Jan 1994).
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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).
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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 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).
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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 sequences
based on the FLASH algorithm (Fast-Lookup Algorithm for Sequence
Homology). Currently operates with SWISS-PROT; will soon also
allows searches in 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).
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Entry : EMS0005
Name : EMBL Network File Server
Organiz. : European Molecular Biology 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 at embl-heidelberg.de
Contact : To report problems: nethelp at embl-heidelberg.de
Status : Tested (26 Jan 1994).
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Entry : EMS0006
Name : EMBL Mail-FASTA Server
Organiz. : European Molecular Biology 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. 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 embl-heidelberg.de
Contact : To report problems: nethelp at embl-heidelberg.de
Status : Tested (26 Jan 1994).
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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).
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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).
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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).
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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).
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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 EMBL 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).
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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).
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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 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 at ford.gatech.edu
Contact : To report problems: mb56 at prism.gatech.edu
or: gt1619a at prism.gatech.edu
Note : To get help you need to send "instructions" as the subject line
of your message.
Status : Tested (26 Jan 1994).
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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).
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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).
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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).
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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).
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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).
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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).
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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 : 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 : EMBL Mail-QUICKSEARCH server
Organiz. : European Molecular Biology 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) ? The databases are updated daily.
Address : quick at embl-heidelberg.de
Contact : To report problems: nethelp at embl-heidelberg.de
Status : Tested (26 Jan 1994).
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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).
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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 agains 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).
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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).
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Entry : EMS0024
Name : TM7 file server
Organiz. : European Molecular Biology Laboratory (EMBL) / Heidelberg /
Germany
Type : RETRIEVAL
Description: The aim is to have all data relevant to G protein-coupled
receptors that possess the 7 transmembrane helical motif.
Address : tm7 at embl-heidelberg.de
Contact : To report problems: vriend at embl-heidelberg.de
Status : Tested (26 Jan 1994).
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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).
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