Bio::Tools::WebBlat(3)

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

SYNOPSIS
  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
  }

DESCRIPTION
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.

AUTHOR
  Allen Day E<lt>allenday@ucla.eduE<gt>

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $obj = new Bio::Tools::WebBlat();
 Function: Builds a new Bio::Tools::WebBlat object
 Returns : an instance of Bio::Tools::WebBlat
 Args    :

  init
 Title   : init
 Usage   : $obj->init(%arg);
 Function: internal method.  initializes a new Bio::Tools::WebBlat object
 Returns : true on success
 Args    : args passed to new()

  create_searchio
  Title   : create_searchio
  Usage   : my $searchio = $obj->create_searchio(%args);
  Function: connects to genome.ucsc.edu and runs a BLAT search against the
            organism/database you specify (see args).  search defaults to
            Human/Hg16
  Returns : returns a Bio::SearchIO object
  Args    : database  (optional) : database to search.  defaults to Hg16.
            organism  (optional) : organism to search.  defaults to Human.
            sequence  (required) : Bio::SeqI object to use in the search.