man : Bio::SeqFeature::Similarity(3p)
Bio::SeqFeature::Similarity(3) User Contributed Perl Documentation
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.
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
bioperl-lATbioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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
AUTHOR - Hilmar Lapp
Email hlappATgmx.net or hilmar.lappATpharma.com
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : significance
Usage : $evalue = $obj->significance();
Title : bits
Usage : $bits = $obj->bits();
Title : frac_identical
Usage : $fracid = $obj->frac_identical();
Title : seqlength
Usage : $len = $obj->seqlength();
Title : seqdesc
Usage : $desc = $obj->seqdesc();
Function: At present this method is a shorthand for
Note that this is not stored in the tag system and hence will
not be included in the return value of gff_string().
perl v5.12.2 February 24, 2011