Provided by: libbio-perl-perl_1.6.923-1_all
Bio::SeqFeature::Similarity - A sequence feature based on similarity
# obtain a similarity feature somehow print "significance: ", $sim_fea->significance(), "\n"; print "bit score: ", $sim_fea->bits(), "\n"; print "score: ", $sim_fea->score(), "\n"; print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
This module is basically a sequence features based on similarity, and therefore has support for measures assessing the similarity. Everything else is inherited from Bio::SeqFeature::Generic.
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AUTHOR - Hilmar Lapp
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Returns : Args : frac_identical Title : frac_identical Usage : $fracid = $obj->frac_identical(); $obj->frac_identical($value); Function: Returns : Args : seqlength Title : seqlength Usage : $len = $obj->seqlength(); $obj->seqlength($len); Function: Returns : Args : seqdesc Title : seqdesc Usage : $desc = $obj->seqdesc(); $obj->seqdesc($desc); Function: At present this method is a shorthand for $obj->annotation()->description(). Note that this is not stored in the tag system and hence will not be included in the return value of gff_string(). Returns : Args :