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bio::matrix::psm::instancesitei(3pm) [debian man page]

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)

Check Out this Related Man Page

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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