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.\" ========================================================================
.\"
.IX Title "TFBS::PatternGen::AnnSpec 3"
.TH TFBS::PatternGen::AnnSpec 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
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.SH "NAME"
TFBS::PatternGen::AnnSpec \- a pattern factory that uses the AnnSpec program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\& my $patterngen =
\& TFBS::PatternGen::AnnSpec\->new(\-seq_file=>\*(Aqsequences.fa\*(Aq,
\& \-binary => \*(Aqann\-spec \*(Aq
\&
\&
\& my $pfm = $patterngen\->pattern(); # $pfm is now a TFBS::Matrix::PFM object
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::PatternGen::AnnSpec builds position frequency matrices
using an external program AnnSpec (Workman, C. and Stormo, G.D. (2000) ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Proc. Pacific Symposium on Biocomputing 2000).
.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::AnnSpec\->new(%args);
\& Function: the constructor for the TFBS::PatternGen::AnnSpec object
\& Returns : a TFBS::PatternGen::AnnSpec 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 \*(Aqann\-spec\*(Aq
\& \-additional_params # a string containing additional
\& # command\-line switches for the
\& # ann\-spec 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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