Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise # Build a Promoterwise alignment factory my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1); my $factory = Bio::Tools::Run::Promoterwise->new(@params); my (@fp)= $factory->run($seq1,$seq2); # each feature pair is a group of hsps foreach my $fp(@fp){ print "Hit Length: ".$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 = $fp->feature2->sub_SeqFeature; for ($i..$#first_hsp){ print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n"; } } print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n"; #Available parameters include: #( S T U V QUERY_START QUERY_END TARGET_START #TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT #LHREJECT LHMAX DYMEM KBYTE DYCACHE) #For an explanation of these parameters, please see documentation #from the Wise package. Promoterwise 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 by Ewan Birney. It is part of the wise2 package available at: http://www.sanger.ac.uk/software/wise2.

Mailing Lists
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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email: shawnh@fugu-sg.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

version
Title : version Usage : exit if $prog->version() < 1.8 Function: Determine the version number of the program Example : Returns : float or undef Args : none

run
Title : run Usage : 2 sequence objects @fp = $factory->run($seq1, $seq2); Function: run Returns : An array of <Bio::SeqFeature::FeaturePair> Args : Name of a file containing a set of 2 fasta sequences or else 2 Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or 2 Bio::Seq objects. If arguments are strings, throws exception if file corresponding to string name can not be found.

_run
Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to a promoterwise program Example : Returns : L<Bio::SeqFeature::FeaturePair> Args : Name of a files containing 2 sequences in the order of peptide and genomic

_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: creates a string of params to be used in the command string Example : Returns : string of params Args :

_query_pep_seq
Title : _query_pep_seq Usage : Internal function, not to be called directly Function: get/set for the query sequence Example : Returns : Args :

_subject_dna_seq
Title : _subject_dna_seq Usage : Internal function, not to be called directly Function: get/set for the subject sequence Example : Returns : Args :