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 :