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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.


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AUTHOR - Hilmar Lapp

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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


 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    :