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 - the query $sim = $sim_pair->hit(); # dto - the hit. # 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.

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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://bugzilla.bioperl.org/ 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 _

new
Title : new Usage : my $similarityPair = new Bio::SeqFeature::SimilarityPair (-hit => $hit, -query => $query, -source => 'blastp'); Function: Initializes a new SimilarityPair object Returns : Bio::SeqFeature::SimilarityPair Args : -query => The query in a Feature pair -hit => (formerly '-subject') the subject/hit in a Feature pair

query
Title : query Usage : $query_feature = $obj->query(); $obj->query($query_feature); Function: The query object for this similarity pair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair

subject
Title : subject Usage : $sbjct_feature = $obj->subject(); $obj->subject($sbjct_feature); Function: Get/Set Subject for a SimilarityPair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity Notes : Deprecated. Use the method 'hit' instead

hit
Title : hit Usage : $sbjct_feature = $obj->hit(); $obj->hit($sbjct_feature); Function: Get/Set Hit for a SimilarityPair Returns : Bio::SeqFeature::Similarity Args : [optional] Bio::SeqFeature::Similarity

source_tag
Title : source_tag Usage : $source = $obj->source_tag(); # i.e., program $obj->source_tag($evalue); Function: Gets the source tag (program name typically) for a feature Returns : string Args : [optional] string

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 :