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@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@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@convex.csc.fi) and Tan Tin Wee (bchtantw@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 ============================================================================== B) LIST OF EMAIL SERVERS ------------------------ ------------------------------------------------------------------------------ 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@net.bio.net Contact : To report problems: biosci@net.bio.net Status : Tested (11 May 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@temin.lanl.gov Contact : To report problems: michael@genome.lanl.gov Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@ncbi.nlm.nih.gov Contact : To report problems: blast-help@ncbi.nlm.nih.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@howard.fhcrc.org Contact : To report problems: jorja@sparky.fhcrc.org Status : Tested (3 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@ed.ac.uk Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@inf.ethz.ch Contact : To report problems: knecht@inf.ethz.ch Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@watson.ibm.com Contact : To report problems: dflash@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 July 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@ncbi.nlm.nih.gov Contact : To report problems: carolyn@ncbi.nlm.nih.gov Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@smlab.eg.gunma-u.ac.jp Contact : To report problems: smiyazaw@smlab.eg.gunma-u.ac.jp Status : Tested (31 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@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). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@genius.embnet.dkfz-heidelberg.de Contact : To report problems: dok248@genius.embnet.dkfz-heidelberg.de Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@genius.embnet.dkfz-heidelberg.de Contact : To report problems: dok248@genius.embnet.dkfz-heidelberg.de Status : Tested (15 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0012 Name : GenMark Organiz. : 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. Status : Tested (30 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@ornl.gov Contact : To report problems: grailmail@ornl.gov Status : Tested (4 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0015 Name : NetGene mail server Organiz. : 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). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@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 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@embl-heidelberg.de Contact : To report problems: predict-help@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@gunbrf.bitnet or fileserv@nbrf.georgetown.edu Contact : To report problems: postmaster@gunbrf.bitnet or postmaster@nbrf.georgetown.edu Status : Tested (4 Jan 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@anl.gov Contact : To report problems: pythia-admin@anl.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@embl-heidelberg.de Contact : To report problems: nethelp@embl-heidelberg.de Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0026 Name : RDP mail server Organiz. : Ribosomal Database Project / University of Illinois Type : RETRIEVAL Description: Access to data and software relative to ribosomal RNA sequences. Address : server@rdp.life.uiuc.edu Contact : To report problems: rdp@phylo.life.uiuc.edu Status : Tested (29 Jul 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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, etc. Address : retrieve@ncbi.nlm.nih.gov Contact : To report problems: retrieve-help@ncbi.nlm.nih.gov Status : Tested (30 Dec 1992). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0023 Name : Springer Journals Preview Service Organiz. : Springer Verlag, Dept. New Technologies 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 abstracts. Address : svjps@dhdspri6.bitnet Contact : To report problems: springer@dhdspri6.bitnet Status : Tested (12 March 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ 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@embl-heidelberg.de Contact : To report problems: vriend@embl-heidelberg.de Status : Tested (30 March 1993). ------------------------------------------------------------------------------ // ------------------------------------------------------------------------------ Entry : EMS0022 Name : University of Houston Gene-Server Organiz. : University of 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@bchs.uh.edu Contact : To report problems: gene-server-management@evolution.bchs.uh.edu Status : Tested (7 Jan 1993). ------------------------------------------------------------------------------ // ============================================================================== =End=of=document==============================================================