Provided by: libbio-perl-perl_1.7.2-3_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.
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: email@example.com rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. 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: https://github.com/bioperl/bioperl-live/issues
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 :