/ 
bioperl-1.5.2-RC3
/ Bio::Tools::WebBlat

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.