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.\"
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.\" ========================================================================
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.\" ========================================================================
.\"
.IX Title "TFBS::PatternGen::MEME 3"
.TH TFBS::PatternGen::MEME 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
TFBS::PatternGen::MEME \- a pattern factory that uses the MEME program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\& my $patterngen =
\& TFBS::PatternGen::MEME\->new(\-seq_file=>\*(Aqsequences.fa\*(Aq,
\& \-binary => \*(Aqmeme\*(Aq
\&
\&
\& my $pfm = $patterngen\->pattern(); # $pfm is now a TFBS::Matrix::PFM object
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::PatternGen::MEME builds position frequency matrices
using an external program \s-1MEME\s0 written by Bailey and Elkan.
For information and source code of \s-1MEME\s0 see
.PP
http://www.sdsc.edu/MEME
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Wynand Alkema"
.IX Header "AUTHOR - Wynand Alkema"
Wynand Alkema <Wynand.Alkema@cgb.ki.se>
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title : new
\& Usage : my $pattrengen = TFBS::PatternGen::MEME\->new(%args);
\& Function: the constructor for the TFBS::PatternGen::MEME object
\& Returns : a TFBS::PatternGen::MEME 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 the \*(Aqmeme\*(Aq executable
\& # OPTIONAL: default \*(Aqmeme\*(Aq
\& \-additional_params # a string containing additional
\& # command\-line switches for the
\& # meme program
.Ve
.SS "pattern"
.IX Subsection "pattern"
.SS "all_patterns"
.IX Subsection "all_patterns"
.SS "patternSet"
.IX Subsection "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.
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