Bio::SeqFeature::SimilarityPair(3pm) User Contributed Perl Documentation Bio::SeqFeature::SimilarityPair(3pm)
NAME
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
SYNOPSIS
$sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
$sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
$sim = $sim_pair->hit(); # dto - the hit.
# some properties for the similarity pair
$expect = $sim_pair->significance();
$score = $sim_pair->score();
$bitscore = $sim_pair->bits();
# this will not write the description for the sequence (only its name)
print $sim_pair->query()->gff_string(), "
";
DESCRIPTION
Lightweight similarity search result as a pair of Similarity features. This class inherits off Bio::SeqFeature::FeaturePair and therefore
implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, with better support for
representing similarity search results in a cleaner way.
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 _
new
Title : new
Usage : my $similarityPair = Bio::SeqFeature::SimilarityPair->new
(-hit => $hit,
-query => $query,
-source => 'blastp');
Function: Initializes a new SimilarityPair object
Returns : Bio::SeqFeature::SimilarityPair
Args : -query => The query in a Feature pair
-hit => (formerly '-subject') the subject/hit in a Feature pair
query
Title : query
Usage : $query_feature = $obj->query();
$obj->query($query_feature);
Function: The query object for this similarity pair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair
subject
Title : subject
Usage : $sbjct_feature = $obj->subject();
$obj->subject($sbjct_feature);
Function: Get/Set Subject for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
Notes : Deprecated. Use the method 'hit' instead
hit
Title : hit
Usage : $sbjct_feature = $obj->hit();
$obj->hit($sbjct_feature);
Function: Get/Set Hit for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
source_tag
Title : source_tag
Usage : $source = $obj->source_tag(); # i.e., program
$obj->source_tag($evalue);
Function: Gets the source tag (program name typically) for a feature
Returns : string
Args : [optional] string
significance
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
score
Title : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
bits
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::SeqFeature::SimilarityPair(3pm)