Bio::SeqFeature::SimilarityPair.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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    :