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libtfbs-perl

scanning DNA sequence with a position weight matrix

Variants:
The TFBS perl modules comprise a set of routines to interact with the Transfac and Jaspar databases that describe a special family of proteins, the transcription factors. These bind to genomic DNA to initiate (or prevent) the readout of a gene. Once multiple binding sites are known for a transcription factor, these are gathered in a single file and are aligned in order to find position-specific characteristica that might be used to predict such binding events in novel DNA sequences.

If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136".

Homepage:
Package version:0.5.svn.20091128-1+b1
Architecture:i386
Distribution:Debian
Filename:libtfbs-perl_0.5.svn.20091128-1+b1_i386.deb

/usr/share/doc/libtfbs-perl/README.Debian

Notes on how this package is tested.
──────────────────────────────────── 

The regression tests of this Perl module are executed at build time. You can
therefore consult the result in the build logs:

https://buildd.debian.org/libtfbs-perl

Network access is not guaranteed in our auto-builder infrastructure. Tests that
depend
more»

/usr/share/man/man3/TFBS::DB::FlatFileDir.3pm.gz

TFBS::DB::FlatFilUser(Contributed Perl DocTFBS::DB::FlatFileDir(3pm)



NAME
       TFBS::DB::FlatFileDir - interface to a database of pattern
       matrices stored as a collection of flat files in a dedicated
       directory

SYNOPSIS
       ·   creating a database object by connecting to the existing
           directory

               my $db = TFBS::DB::FlatFileDir->connect("/home/boris/Mat
more»

/usr/share/man/man3/TFBS::DB::JASPAR2.3pm.gz

TFBS::DB::JASPAR2User)Contributed Perl DocumenTFBS::DB::JASPAR2(3pm)



NAME
       TFBS::DB::JASPAR2 - interface to MySQL relational database of
       pattern matrices

SYNOPSIS
       ·   creating a database object by connecting to the existing
           JASPAR2-type database

               my $db = TFBS::DB::JASPAR2->connect("dbi:mysql:JASPAR2:myhost",
                                      
more»

/usr/share/man/man3/TFBS::DB::JASPAR4.3pm.gz

TFBS::DB::JASPAR4User)Contributed Perl DocumenTFBS::DB::JASPAR4(3pm)



NAME
       TFBS::DB::JASPAR
more»

/usr/share/man/man3/TFBS::DB::JASPAR5.3pm.gz

TFBS::DB::JASPAR5User)Contributed Perl DocumenTFBS::DB::JASPAR5(3pm)



NAME
       TFBS::DB::JASPAR
more»

/usr/share/man/man3/TFBS::DB::LocalTRANSFAC.3pm.gz

TFBS::DB::LocalTRUserAContributed Perl DTFBS::DB::LocalTRANSFAC(3pm)



NAME
       TFBS::DB::LocalT
more»

/usr/share/man/man3/TFBS::DB::TRANSFAC.3pm.gz

TFBS::DB::TRANSFAUsermContributed Perl DocumeTFBS::DB::TRANSFAC(3pm)



NAME
       TFBS::DB::TRANSF
more»

/usr/share/man/man3/TFBS::Ext::pwmsearch.3pm.gz

pwmsearch(3pm)   User Contributed Perl Documentation  pwmsearch(3pm)



NAME
       TFBS::Ext::pwmse
more»

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