---
name: "Bio::SeqFeature::SimilarityPair"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::SeqFeature::SimilarityPair"
---

# Bio::SeqFeature::SimilarityPair(3pm)

Sequence feature based on the similarity of two sequences.

## 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
```

### 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    :
```