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Manual Reference Pages  -  BIO::SEQFEATURE::SIMILARITYPAIR (3)

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NAME

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

CONTENTS

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    :



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perl v5.20.3 BIO::SEQFEATURE::SIMILARITYPAIR (3) 2016-04-05

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