From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!spool.mu.edu!uunet!biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!blitz Tue Jan 12 12:30:01 EST 1993
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From: blitz@embl-heidelberg.de
Newsgroups: bionet.general,bionet.molbio.embldatabank
Subject: MPsrch:  announcing a new service.
Message-ID: <1993Jan12.175048.63351@embl-heidelberg.de>
Date: 12 Jan 93 16:50:48 GMT
Organization: EMBL, European Molecular Biology Laboratory
Lines: 65


                             MPsrch
                             ------

       (C) Biocomputing Research Unit, University of Edinburgh, 1992

     Smith and Waterman Protein Sequence Database searches on a MasPar  


  MPsrch (by Shane Sturrock and John Collins), the fastest implementation
  of the exhaustive Best Local Similarity algorithm for Sequence Database
  searching, is now available through BLITZ, a new e-mail service from the
  EMBL.  MPsrch runs on the 4096-processor MasPar MP-1 machine at the EMBL,
  using the Smith & Waterman algorithm, performing up to 140,000,000 cell
  updates per second.

    Typical search times on the MasPar against Swiss-Prot 23 are:

  5037 residues  RYNR_RABIT  340 seconds  (134,000,000 cell updates/second)
   377   "       ACTS_HUMAN   40 seconds  ( 85,000,000 cell updates/second)


  To get current help information, e-mail the word HELP in a mail message to
  the Internet address:

	Blitz@EMBL-Heidelberg.DE


  To run a search, using default weight matrix and INDEL cost settings, try
  sending an e-mail message with the word SEQ on the first line and the 
  sequence in free format on succeeding lines.   The end of the sequence is 
  determined either by the end of your mail message, if you do not use an 
  automatic mail signature, or by inserting a new line beginning with the 
  word END. 
  For example:

SEQ
	STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL
	FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE
	YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM
	TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ
	VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG
END


  The Help information explains how you can specify a PAM matrix between 1
  and 500 PAM's, an INDEL cost and the number of alignments to be returned
  in the output.

  The sensitivity of MPsrch depends on the choice of parameters, and
  searches with default parameter settings alone may not always find the
  most interesting results.  Even with the same query sequence, one set of
  parameters may find strong alignments best, while a different setting may
  show up weaker relationships better.  Because the search is so fast, we would
  encourage you to experiment with your own choice of parameter settings.

  In future developments, we hope to provide searches of other databases,
  including a nucleotide search facility.  


  John Collins & Shane Sturrock,                      Des Higgins (Data Library)
  Biocomputing Research Unit,                       & Roy Omond (Computer Group)
  University of Edinburgh,                            EMBL,
  Scotland,                                           Heidelberg,
  U.K.                                                Germany.


.