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Bio::SeqFeature::SimilarityPair(3) User Contributed Perl Documentation Bio::SeqFeature::SimilarityPair(3)

Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.

  $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($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";

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.

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.                  - General discussion  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
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:

Email or

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 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

 Title   : query
 Usage   : $query_feature = $obj->query();
 Function: The query object for this similarity pair
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity
See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair

 Title   : subject
 Usage   : $sbjct_feature = $obj->subject();
 Function: Get/Set Subject for a SimilarityPair 
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity
 Notes   : Deprecated.  Use the method 'hit' instead

 Title   : hit
 Usage   : $sbjct_feature = $obj->hit();
 Function: Get/Set Hit for a SimilarityPair 
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity

 Title   : source_tag
 Usage   : $source = $obj->source_tag(); # i.e., program
 Function: Gets the source tag (program name typically) for a feature 
 Returns : string
 Args    : [optional] string

 Title   : significance
 Usage   : $evalue = $obj->significance();
 Returns : 
 Args    :

 Title   : score
 Usage   : $score = $obj->score();
 Returns : 
 Args    :

 Title   : bits
 Usage   : $bits = $obj->bits();
 Returns : 
 Args    :
2019-01-01 perl v5.28.1

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