NAME

XMS::Motif - Perl module for creating DNA motifs in XMS format

SYNOPSIS

use XMS::Motif;

my $motif = XMS::Motif->new($wm,$name,$threshold) # $wm is weightmatrix, $name is name of the motif and $threshold is the threshold value. $motif -> toXML() # Create motifs in XMS format $motif -> toString() # Create motifs in string/xms format

DESCRIPTION

The XMS::Motif package can be used to create the XMS format for a given set of motifs, their asscoiated weightmatrices and threshold values.

METHODS XMS::Motif provides four methods, new(), toXML(), toString() and weblogo():

$w = XMS::Motif-new([list]);>

new() returns a new String handle.

$x = $w-toXML();>

toXML() converts the weightmatrix into a XMS format.

$s = $w-toString();>

toString() converts the weightmatrix into a string.

$logo = $w-weblogo();> weblogo() creates a graphic weblogo (png file) for a motif. It depends on the TFBS::Matrix perl module.

DEPENDENCIES

This module has external dependencies on the following modules: Exporter XML::Writer, IO::File XMS::WeightMatrix

EXPORT

Nothing.

SEE ALSO

perl(1), XML::Writer, XMS::WeightMatrix, XMS::MotifSet

AUTHOR

Harpreet Saini, hsaini@ebi.ac.uk

COPYRIGHT AND LICENSE

Copyright (C) 2009 by harpreet saini

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.9 or, at your option, any later version of Perl 5 you may have available.