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.\" ========================================================================
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.\" ========================================================================
.\"
.IX Title "TFBS::DB::TRANSFAC 3"
.TH TFBS::DB::TRANSFAC 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.
.if n .ad l
.nh
.SH "NAME"
TFBS::DB::TRANSFAC \- interface to database of TRANSFAC public
position frequency matrices at TESS (http://www.cbil.upenn.edu/tess)
.PP
.Vb 5
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- NOTICE \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
\& The TRANSFAC database is free for non\-commercial use. For commercial use
\& the TRANSFAC databases and programs have to be licensed. Please read
\& the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm.
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.Ve
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.IP "\(bu" 4
creating a database object by connecting to \s-1TRANSFAC\s0 data
.Sp
.Vb 1
\& my $db = TFBS::DB::TRANSFAC\->connect();
.Ve
.IP "\(bu" 4
retrieving a TFBS::Matrix::* object from the database
.Sp
.Vb 2
\& # retrieving a PFM by ID
\& my $pfm = $db\->get_Matrix_by_ID(\*(AqV$CEBPA_01\*(Aq,\*(AqPFM\*(Aq);
\&
\& #retrieving a PWM by TRANSFAC accession number
\& my $pwm = $db\->get_Matrix_by_acc(\*(AqM00116\*(Aq, \*(AqPWM\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1TFBS::DB::TRANSFAC\s0 is a read only database interface that fetches
\&\s-1TRANSFAC\s0 matrix data from \s-1TESS\s0 web interface
(http://www.cbil.upen.edu/TESS) and returns TFBS::Matrix::* objects.
.SS "connect"
.IX Subsection "connect"
.Vb 10
\& Title : connect
\& Usage : my $db = TFBS::DB::TRANSFAC\->connect(%args);
\& Function: Creates a TRANSFAC database connection object, which can be used
\& to retrieve matrices from public TRANSFAC databases via the web
\& Returns : a TFBS::DB::TRANSFAC object
\& Args : \-proxy # OPTIONAL: a http proxy server name,
\& # usually required for accessing TRANSFAC from behind
\& # a firewall
\& \-accept_conditions # OPTIONAL: by setting this to a true
\& # value, you confirm that you
\& # have read and accepted the terms
\& # of use of TRANSFAC at
\& # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
\& # this also suppresses the annoying
\& # message that is printed to STDERR
\& # upon invoking the method
.Ve
.SS "new"
.IX Subsection "new"
.Vb 7
\& Title : connect
\& Usage : my $db = TFBS::DB::TRANSFAC\->connect(%args);
\& Function: Here, I<new> is just a synonim for I<connect>
\& (to make the interface consistent with other
\& bioperl read\-obly Bio::DB::* objects)
\& Returns : a TFBS::DB::TRANSFAC object
\& Args : \-accept_conditions # see explanation at I<new>
.Ve
.SS "get_Matrix_by_ID"
.IX Subsection "get_Matrix_by_ID"
.Vb 10
\& Title : get_Matrix_by_ID
\& Usage : my $pfm = $db\->get_Matrix_by_ID(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
\& Function: fetches matrix data under the given TRANSFAC ID from the
\& database and returns a TFBS::Matrix::* object
\& Returns : a TFBS::Matrix::* object; the exact type of the
\& object depending on the second argument (allowed
\& values are \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq); returns undef if
\& matrix with the given ID is not found
\& Args : (Matrix_ID, Matrix_type)
\& Matrix_ID is a string; Matrix_type is one of the
\& following: \*(AqPFM\*(Aq (raw position frequency matrix),
\& \*(AqICM\*(Aq (information content matrix) or \*(AqPWM\*(Aq (position
\& weight matrix)
\& If Matrix_type is omitted, a PFM is retrieved by default.
.Ve
.SS "get_Matrix_by_acc"
.IX Subsection "get_Matrix_by_acc"
.Vb 10
\& Title : get_Matrix_by_acc
\& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
\& Function: fetches matrix data under the given TRANSFAC accession number
\& from database and returns a TFBS::Matrix::* object
\& Returns : a TFBS::Matrix::* object; the exact type of the
\& object depending on the second argument (allowed
\& values are \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq); returns undef if
\& matrix with the given ID is not found
\& Args : (Matrix_ID, Matrix_type)
\& Matrix_ID is a string; Matrix_type is one of the
\& following: \*(AqPFM\*(Aq (raw position frequency matrix),
\& \*(AqICM\*(Aq (information content matrix) or \*(AqPWM\*(Aq (position
\& weight matrix)
\& If Matrix_type is omitted, a PFM is retrieved by default.
.Ve
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