pwmsearch(3pm) User Contributed Perl Documentation pwmsearch(3pm)NAME
TFBS::Ext::pwmsearch - Perl extension for scanning a DNA sequence object with a position weight matrix
SYNOPSIS
use TFBS::Ext::pwmsearch;
pwmsearch
DESCRIPTION
Stub documentation for TFBS::Ext::pwmsearch, created by h2xs. It looks like the author of the extension was negligent enough to leave the
stub unedited.
Blah blah blah.
EXPORT
None by default.
AUTHOR
A. U. Thor, a.u.thor@a.galaxy.far.far.away
SEE ALSO perl(1).
perl v5.14.2 2008-01-24 pwmsearch(3pm)
Check Out this Related Man Page
TFBS::PatternGen::Elph(3pm) User Contributed Perl Documentation TFBS::PatternGen::Elph(3pm)NAME
TFBS::PatternGen::Elph - a pattern factory that uses the Elph program
SYNOPSIS
my $patterngen =
TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
-binary => '/Elph/elph'
-motif_length => [8, 9, 10],
-additional_params => '-x -r -e');
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs sampling algorithm implemented in external Gibbs program
by Chip Lawrence. The algorithm can produce multiple patterns from a single set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::Gibbs->new(%args);
Function: the constructor for the TFBS::PatternGen::Gibbs object
Returns : a TFBS::PatternGen::Gibbs object
Args : This method takes named arguments;
you must specify one of the following three
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
Other arguments are:
-binary # a fully qualified path to Gibbs executable
# OPTIONAL: default 'Gibbs'
-nr_hits # a presumed number of pattern occurences in the
# sequence set: it can be a single integer, e.g.
# -nr_hits => 24 , or a reference to an array of
# integers, e.g -nr_hits => [12, 24, 36]
-motif_length # an expected length of motif in nucleotides:
# it can be a single integer, e.g.
# -motif_length => 8 , or a reference to an
# array ofintegers, e.g -motif_length => [8..12]
-additional_params # a string containing additional
# command-line switches for the
# Gibbs program
pattern
all_patterns
patternSet
The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::Elph(3pm)
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