Bio::Map::TranscriptionFactor(3pm) User Contributed Perl Documentation Bio::Map::TranscriptionFactor(3pm)
NAME
Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable element
SYNOPSIS
use Bio::Map::TranscriptionFactor;
use Bio::Map::GeneMap;
use Bio::Map::Position;
# model a TF that binds 500bp upstream of the BRCA2 gene in humans and
# 250bp upstream of BRCA2 in mice
my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
my $map1 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
-species => "human");
my $map2 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
-species => "mouse");
Bio::Map::Position->new(-map => $map1,
-element => $tf,
-start => -500,
-length => 10);
Bio::Map::Position->new(-map => $map2,
-element => $tf,
-start => -250,
-length => 10);
# Find out where the transcription factor binds
foreach $pos ($tf->get_positions) {
print $tf->universal_name, " binds at position " $pos->value, " relative to ",
$pos->relative->description, " of gene ",
$pos->map->universal_name, " in species ", $pos->map->species, "
";
}
DESCRIPTION
A transcription factor modelled as a mappable element. It can have mulitple binding sites (positions) near multiple genes (maps).
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $tf = Bio::Map::TranscriptionFactor->new();
Function: Builds a new Bio::Map::TranscriptionFactor object
Returns : Bio::Map::TranscriptionFactor
Args : -universal_name => string name of the TF (in a form common to all
species that have the TF, but unique amongst
non-orthologous TFs), REQUIRED
-description => string, free text description of the TF
get
Title : get
Usage : my $obj = Bio::Map::TranscriptionFactor->get();
Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or
gets a pre-existing one that shares the same universal_name.
Returns : Bio::Map::TranscriptionFactor
Args : -universal_name => string name of the TF (in a form common to all
species that have the TF, but unique amongst
non-orthologous TFs), REQUIRED
-description => string, free text description of the TF
universal_name
Title : universal_name
Usage : my $name = $obj->universal_name
Function: Get/Set TF name, corresponding to the name of the TF in a form shared
by orthologous versions of the TF in different species, but otherwise
unique.
Returns : string
Args : none to get, OR string to set
description
Title : description
Usage : my $desc = $obj->description
Function: Get/Set a description of the TF.
Returns : string
Args : none to get, OR string to set
perl v5.14.2 2012-03-02 Bio::Map::TranscriptionFactor(3pm)