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bio::seqfeature::similarity(3pm) [debian man page]

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

NAME
Bio::SeqFeature::Similarity - A sequence feature based on similarity SYNOPSIS
# obtain a similarity feature somehow print "significance: ", $sim_fea->significance(), " "; print "bit score: ", $sim_fea->bits(), " "; print "score: ", $sim_fea->score(), " "; print "fraction of identical residues: ", $sim_fea->frac_identical(), " "; DESCRIPTION
This module is basically a sequence features based on similarity, and therefore has support for measures assessing the similarity. Everything else is inherited from Bio::SeqFeature::Generic. 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 _ significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : bits Title : bits Usage : $bits = $obj->bits(); $obj->bits($value); Function: Returns : Args : frac_identical Title : frac_identical Usage : $fracid = $obj->frac_identical(); $obj->frac_identical($value); Function: Returns : Args : seqlength Title : seqlength Usage : $len = $obj->seqlength(); $obj->seqlength($len); Function: Returns : Args : seqdesc Title : seqdesc Usage : $desc = $obj->seqdesc(); $obj->seqdesc($desc); Function: At present this method is a shorthand for $obj->annotation()->description(). Note that this is not stored in the tag system and hence will not be included in the return value of gff_string(). Returns : Args : perl v5.14.2 2012-03-02 Bio::SeqFeature::Similarity(3pm)

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

NAME
Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches SYNOPSIS
# get a Set object probably from the results object print "Bits score over set ",$set->bits," evalue ",$set->evalue," "; foreach $domain ( $set->each_Domain ) { print "Domain start ",$domain->start," end ",$domain->end," "; } DESCRIPTION
Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these attributes are also on the per domain scores, which you can get there). 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 - Ewan Birney Email birney-at-ebi.ac.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ add_Domain Title : add_Domain Usage : $set->add_Domain($domain) Function: adds the domain to the list Returns : nothing Args : A Bio::Tools::HMMER::Domain object each_Domain Title : each_Domain Usage : foreach $domain ( $set->each_Domain() ) Function: returns an array of domain objects in this set Returns : array Args : none name Title : name Usage : $obj->name($newval) Function: Example : Returns : value of name Args : newvalue (optional) desc Title : desc Usage : $obj->desc($newval) Function: Example : Returns : value of desc Args : newvalue (optional) accession Title : accession Usage : $obj->accession($newval) Function: Example : Returns : value of accession Args : newvalue (optional) bits Title : bits Usage : $obj->bits($newval) Function: Example : Returns : value of bits Args : newvalue (optional) evalue Title : evalue Usage : $obj->evalue($newval) Function: Example : Returns : value of evalue Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::Tools::HMMER::Set(3pm)
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