[Bioperl-l] new module: Bio::Tools::WebBlat

Allen Day allenday at ucla.edu
Sat Apr 17 04:31:49 EDT 2004

added a new module to bioperl-live for running BLAT jobs from a UCSC CGI 
script.  i didn't want to go to the hassle of setting up my own BLAT 
server, so here you go.  Docs below, enjoy.



Bio::Tools::WebBlat - Run BLAT on UCSC CGI script


  my $webblat = Bio::Tools::WebBlat->new();
  my $seq = Bio::Seq->new(display_id => 'foo' , seq => 'aataataat');
  my $searchio = $webblat->create_searchio($seq);

  while(my $result = $searchio->next_result){
    #process Bio::SearchIO::ResultI


Run BLAT at UCSC.  The useful method in this class after instantiation
is create_searchio.  This factory method takes a Bio::Seq object as
input, reformats it as Fasta, and sends it off to a CGI script running
at www.genome.ucsc.edu.  The resultant PSL embedded in HTML is
HTML-stripped and used to construct a Bio::SearchIO, which is passed
back to the user.


Allen Day <allenday at ucla.edu>

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