| Bio::SeqFeature::Similarity(3pm) | User Contributed Perl Documentation | Bio::SeqFeature::Similarity(3pm) |
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
appreciated.
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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.
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:
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
Title : frac_identical
Usage : $fracid = $obj->frac_identical();
$obj->frac_identical($value);
Function:
Returns :
Args :
Title : seqlength
Usage : $len = $obj->seqlength();
$obj->seqlength($len);
Function:
Returns :
Args :
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 :
| 2018-10-27 | perl v5.26.2 |