/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqFeature::SimilarityPair

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(), "\n";

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://github.com/bioperl/bioperl-live/issues

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    :