Bio::Tools::Promoterwise - DESCRIPTION of Object use Bio::Tools::Promoterwise; my $pw = Bio::Tools::Promoterwise->new(-file=>"out", -query1_seq=>$seq1, -query2_seq=>$seq2); while (my $fp = $pw->next_result){ print "Hit Length: ".$fp->feature1->length."\n"; print "Hit Start: ".$fp->feature1->start."\n"; print "Hit End: ".$fp->feature1->end."\n"; print "Hsps: \n"; my @first_hsp = $fp->feature1->sub_SeqFeature; my @second_hsp = $fp->feature2->sub_SeqFeature; foreach my $i (0..$#first_hsp){ print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ". $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n"; } } Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for promoter sequence alignments. Promoterwise is written by Ewan Birney. It is part of the wise2 package available at: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ This module is the parser for the Promoterwise output in tab format.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org Describe contact details here Additional contributors names and emails here 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::Promoterwise(); Function: Builds a new Bio::Tools::Promoterwise object Returns : L<Bio::Tools::Promoterwise> Args : -fh/-file => $val, # for initing input, see Bio::Root::IO

next_result
Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : an L<Bio::SeqFeature::FeaturePair> Args : none