BLAZE still available?

Dan Jacobson danj at welchgate.welch.jhu.edu
Wed Jan 13 10:53:55 EST 1993


In article <1993Jan12.141217.19512 at nuscc.nus.sg> bchtantw at nuscc.nus.sg (Dr Tan Tin Wee) writes:
>
>Is the BLAZE server still available to network users?
>TinWee.
>
The old Blaze server is no longer available for free - but I believe
that Blaze is still available for pay through the IG services.  However,
it is funny that you should mention this today as the following announcement
just came across in bionet.general.  It's a Smith & Waterman running 
on a MasPar - so it's probably the type of thing that you're looking
for.

Best of luck,

Dan Jacobson

================================CLIP=======================================


                             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 at 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.
                                                                              
===================================CLIP========================================




More information about the Bio-soft mailing list