TFBS::Word(3pm) User Contributed Perl Documentation TFBS::Word(3pm)NAME
TFBS::Word - base class for word-based patterns
DESCRIPTION
TFBS::Word is a base class consisting of universal constructor called by its subclasses (TFBS::Matrix::*), and word pattern manipulation
methods that are independent of the word type. It is not meant to be instantiated itself.
FEEDBACK
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.
new
word
validate_word
Required in all subclasses
length
search_seq
search_aln
perl v5.14.2 2008-01-24 TFBS::Word(3pm)
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TFBS::PatternGen::Gibbs::Motif(3pm) User Contributed Perl Documentation TFBS::PatternGen::Gibbs::Motif(3pm)NAME
TFBS::PatternGen::Gibbs::Motif - class for unprocessed motifs and associated numerical scores created by the Gibbs program
SYNOPSIS DESCRIPTION
TFBS::PatternGen::Gibbs::Motif is used to store and manipulate unprocessed motifs and associated numerical scores created by the Gibbs
program. You do not normally want to create a TFBS::PatternGen::Gibbs::Motif yourself. They are created by running TFBS::PatternGen::Gibbs
FEEDBACK
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard and Wynand Alkema
Boris Lenhard <Boris.Lenhard@cgb.ki.se> Wynand Alkema <Wynand.Alkema@cgb.ki.se>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.
MAP
Title : MAP
Usage : my $map_score = $motif->MAP;
Function: returns MAP score for the detected motif
(This is a backward compatibility method. For consistency,
you should use $motif->tag('MAP_score') instead
Returns : float (a scalar)
Args : none
Other methods
TFBS::PatterGen::Motif::Gibbs inherits from TFBS::PatternGen::Motif, which inherits from TFBS::Matrix. Please consult the documentation of
those modules for additional available methods.
perl v5.14.2 2008-01-24 TFBS::PatternGen::Gibbs::Motif(3pm)
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