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motif reqired for hp-ux 11.11
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Bio::Matrix::PSM::InstanceSiteI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::InstanceSiteI(3pm) NAME
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM SYNOPSIS
use Bio::Matrix::PSM::InstanceSite; #Y ou can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq => 'TATAAT', id => "TATAbox1", accession => 'ENSG00000122304', mid => 'TB1', desc => 'TATA box, experimentally verified in PRM1 gene', relpos => -35); DESCRIPTION
Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really unique combination. 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 - Stefan Kirov Email skirov@utk.edu SEE ALSO
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO APPENDIX
mid Title : mid Usage : my $mid=$instance->mid; Function: Get/Set the motif id Throws : Returns : scalar Args : scalar score Title : score Usage : my $score=$instance->score; Function: Get/Set the score (mismatches) between the instance and the attached (or initial) PSM Throws : Returns : real number Args : real number start Title : start Usage : my $start=$instance->start; Function: Get/Set the position of the instance on the sequence used Throws : Returns : integer Args : integer relpos Title : relpos Usage : my $seqpos=$instance->relpos; Function: Get/Set the relative position of the instance with respect to the transcription start site (if known). Can and usually is negative. Throws : Returns : integer Args : integer minstance Title : minstance Usage : my $minstance=$misntance->score; Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox. Not necessarily human readable. Throws : Returns : string Args : string perl v5.14.2 2012-03-02 Bio::Matrix::PSM::InstanceSiteI(3pm)
motif reqired for hp-ux 11.11