.\" -*- mode: troff; coding: utf-8 -*- .\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>. .ie n \{\ . ds C` "" . ds C' "" 'br\} .el\{\ . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "TFBS::DB::TRANSFAC 3pm" .TH TFBS::DB::TRANSFAC 3pm 2024-03-13 "perl v5.38.2" "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 TRANSFAC 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" TFBS::DB::TRANSFAC is a read only database interface that fetches TRANSFAC matrix data from TESS 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 is just a synonim for I \& (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 .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