bio::tools::hmmer::domain(3pm) [debian man page]

Bio::Tools::HMMER::Domain(3pm)				User Contributed Perl Documentation			    Bio::Tools::HMMER::Domain(3pm)

NAME

       Bio::Tools::HMMER::Domain - One particular domain hit from HMMER

SYNOPSIS

       Read the Bio::Tools::HMMER::Results docs

DESCRIPTION

       A particular domain score. We reuse the Homol SeqFeature system here, so this inherits off Homol SeqFeature. As this code originally came
       from a separate project, there are some backward compatibility stuff provided to keep this working with old code.

       Don't forget this inherits off Bio::SeqFeature, so all your usual nice start/end/score stuff is ready for use.

CONTACT

       Ewan Birney, birney@ebi.ac.uk

CONTRIBUTORS

       Jason Stajich, jason@bioperl.org

APPENDIX

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

   add_alignment_line
	Title	: add_alignment_line
	Usage	: $domain->add_alignment_line($line_from_hmmer_output);
	Function: add an alignment line to this Domain object
	Returns : Nothing
	Args	: scalar

	Adds an alignment line, mainly for storing the HMMER alignments
       as flat text which can be reguritated. You're right. This is *not
       nice* and not the right way to do it.  C'est la vie.

   each_alignment_line
	Title	: each_alignment_line
	Usage	: foreach $line ( $domain->each_alignment_line )
	Function: reguritates the alignment lines as they were fed in.
		  only useful realistically for printing.
	Example :
	Returns :
	Args	: None

   get_nse
	Title	: get_nse
	Usage	: $domain->get_nse()
	Function: Provides a seqname/start-end format, useful
		  for unique keys. nse stands for name-start-end
		  It is used a lot in Pfam
	Example :
	Returns : A string
	Args	: Optional separator 1 and separator 2 (default / and -)

   hmmacc
	Title	: hmmacc
	Usage	: $domain->hmmacc($newacc)
	Function: set get for HMM accession number. This is placed in the homol
		  feature of the HMM
	Example :
	Returns :
	Args	:

   hmmname
	Title	: hmmname
	Usage	: $domain->hmmname($newname)
	Function: set get for HMM accession number. This is placed in the homol
		  feature of the HMM
	Example :
	Returns :
	Args	:

   bits
	Title	: bits
	Usage	:
	Function: backward compatibility. Same as score
	Example :
	Returns :
	Args	:

   evalue
	Title	: evalue
	Usage	:
	Function: $domain->evalue($value);
	Example :
	Returns :
	Args	:

   seqbits
	Title	: seqbits
	Usage	:
	Function: $domain->seqbits($value);
	Example :
	Returns :
	Args	:

   seq_range
	Title	: seq_range
	Usage	:
	Function: Throws an exception to catch scripts which need to upgrade
	Example :
	Returns :
	Args	:

   hmm_range
	Title	: hmm_range
	Usage	:
	Function: Throws an exception to catch scripts which need to upgrade
	Example :
	Returns :
	Args	:

perl v5.14.2							    2012-03-02					    Bio::Tools::HMMER::Domain(3pm)

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

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(), "
";

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://redmine.open-bio.org/projects/bioperl/

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	:

perl v5.14.2							    2012-03-02				      Bio::SeqFeature::SimilarityPair(3pm)