Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences. $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit); $sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object $sim = $sim_pair->subject(); # dto. # some properties for the similarity pair $expect = $sim_pair->significance(); $score = $sim_pair->score(); $bitscore = $sim_pair->bits(); # this will not write the description for the sequence (only its name) print $sim_pair->query()->gff_string(), "\n"; Lightweight similarity search result as a pair of Similarity features. This class inherits off Bio::SeqFeature::FeaturePair and therefore implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, with better support for representing similarity search results in a cleaner way.

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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

from_searchResult
Title : from_searchResult Usage : $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blast_obj); $sim_pair->from_searchResult($blast_obj); Function: This method creates or fills SimilarityPair objects from objects representing similarity search results. Since there is no public interface search result objects are required to implement, this method basically checks for the type of the object and dispatches the actual SimilarityPair creation to a method capable of this. At present, the following classes are recognized: Bio::Tools::Blast::Sbjct Bio::Tools::Blast::HSP An exception will be thrown if an object of an unrecognized class is passed. Note that this is probably the point where you will want to add your class if you have a method for creating SimilarityPair objects from it. Note that passing an object that has already previously been filled is potentially error-prone, because undefined fields will not be (re-)set to an undef value. Returns : The object created or filled. Args :

_from_blastObject
Title : from_blastObject Usage : $sim_pair = Bio::SeqFeature::SimilarityPair->_from_blastObj($blast_obj); $sim_pair->_from_blastObj($blast_obj); Function: See documentation for from_searchResult(). This one handles Bio::Tools::Blast::Sbjct and Bio::Tools::Blast::HSP objects. Returns : A SimilarityPair object. Args :

query
Title : query Usage : $query_feature = $obj->query(); $obj->query($query_feature); Function: Returns : Args :

subject
Title : subject Usage : $sbjct_feature = $obj->subject(); $obj->subject($sbjct_feature); Function: Returns : Args :

source_tag
Title : source_tag Usage : $source = $obj->source_tag(); # i.e., program $obj->source_tag($evalue); Function: Returns : Args :

significance
Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args :

score
Title : score Usage : $score = $obj->score(); $obj->score($value); Function: Returns : Args :

bits
Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Returns : Args : of two sequences."