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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeature::Similarity

NAME

Bio::SeqFeature::Similarity - A sequence feature based on similarity

SYNOPSIS

# 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";

DESCRIPTION

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.

FEEDBACK

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.

bioperl-l@bioperl.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:

bioperl-l@bioperl.org

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp

Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com

APPENDIX

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    :