libtfbs-perl_0.6.1+dfsg-1+b1_amd64.deb


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Description

libtfbs-perl - scanning DNA sequence with a position weight matrix

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: libtfbs-perl
Package version: 0.6.1+dfsg
Package release: 1+b1
Package architecture: amd64
Package type: deb
Installed size: 720 B
Download size: 228.04 KB
Official Mirror: ftp.br.debian.org
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".

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    Download

    Source package: libtfbs-perl

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install libtfbs-perl deb package:
      # sudo apt-get install libtfbs-perl

    Files

    • /usr/lib/x86_64-linux-gnu/perl5/5.20/pwm_search.h
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/pwm_searchPFF.c
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/ConservationProfile.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/MatrixSet.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGenI.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternI.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/README.md
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Site.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/SitePair.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/SitePairSet.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/SiteSet.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Word.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/_Iterator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/FlatFileDir.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/JASPAR2.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/JASPAR4.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/JASPAR5.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/JASPAR6.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/LocalTRANSFAC.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/DB/TRANSFAC.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Ext/pwmsearch.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix/Alignment.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix/ICM.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix/PFM.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix/PWM.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Matrix/_Alignment.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/AnnSpec.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Elph.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Gibbs.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/MEME.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/SimplePFM.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/YMF.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/AnnSpec/Motif.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Elph/Motif.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Gibbs/Motif.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/MEME/Motif.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Motif/Matrix.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/Motif/Word.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/PatternGen/YMF/Motif.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Run/ConservationProfileGenerator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Tools/SetOperations.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Word/Consensus.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/_Iterator/_MatrixSetIterator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/_Iterator/_SiteSetIterator.pm
    • /usr/lib/x86_64-linux-gnu/perl5/5.20/auto/TFBS/Ext/pwmsearch/pwmsearch.so
    • /usr/share/doc/libtfbs-perl/README.Debian
    • /usr/share/doc/libtfbs-perl/changelog.Debian.amd64.gz
    • /usr/share/doc/libtfbs-perl/changelog.Debian.gz
    • /usr/share/doc/libtfbs-perl/changelog.gz
    • /usr/share/doc/libtfbs-perl/copyright
    • /usr/share/doc/libtfbs-perl/examples/Ext/t/pwmsearch.t
    • /usr/share/doc/libtfbs-perl/examples/Ext/t/test.fa.gz
    • /usr/share/doc/libtfbs-perl/examples/t/01_Matrix.t
    • /usr/share/doc/libtfbs-perl/examples/t/02_Search.t
    • /usr/share/doc/libtfbs-perl/examples/t/03_DB_FlatFileDir.t
    • /usr/share/doc/libtfbs-perl/examples/t/04_DB_TRANSFAC.t
    • /usr/share/doc/libtfbs-perl/examples/t/05_DB_JASPAR.t
    • /usr/share/doc/libtfbs-perl/examples/t/06_SimplePFM.t
    • /usr/share/doc/libtfbs-perl/examples/t/07_AnnSpec.t
    • /usr/share/doc/libtfbs-perl/examples/t/07_Elph.t
    • /usr/share/doc/libtfbs-perl/examples/t/07_Gibbs.t
    • /usr/share/doc/libtfbs-perl/examples/t/07_MEME.t
    • /usr/share/doc/libtfbs-perl/examples/t/08_DB_LocalTRANSFAC.t
    • /usr/share/doc/libtfbs-perl/examples/t/09_Word_Consensus.t
    • /usr/share/doc/libtfbs-perl/examples/t/10_Tools_SetOperations.t
    • /usr/share/doc/libtfbs-perl/examples/t/test.aln.gz
    • /usr/share/doc/libtfbs-perl/examples/t/test.fa.gz
    • /usr/share/doc/libtfbs-perl/examples/t/test.gibbin.gz
    • /usr/share/doc/libtfbs-perl/examples/t/test_meme.fa.gz
    • /usr/share/doc/libtfbs-perl/examples/t/transfac_new/matrix.dat
    • /usr/share/doc/libtfbs-perl/examples/t/transfac_old/matrix.dat.gz
    • /usr/share/man/man3/TFBS::DB::FlatFileDir.3pm.gz
    • /usr/share/man/man3/TFBS::DB::JASPAR2.3pm.gz
    • /usr/share/man/man3/TFBS::DB::JASPAR4.3pm.gz
    • /usr/share/man/man3/TFBS::DB::JASPAR5.3pm.gz
    • /usr/share/man/man3/TFBS::DB::JASPAR6.3pm.gz
    • /usr/share/man/man3/TFBS::DB::LocalTRANSFAC.3pm.gz
    • /usr/share/man/man3/TFBS::DB::TRANSFAC.3pm.gz
    • /usr/share/man/man3/TFBS::Ext::pwmsearch.3pm.gz
    • /usr/share/man/man3/TFBS::Matrix.3pm.gz
    • /usr/share/man/man3/TFBS::Matrix::Alignment.3pm.gz
    • /usr/share/man/man3/TFBS::Matrix::ICM.3pm.gz
    • /usr/share/man/man3/TFBS::Matrix::PFM.3pm.gz
    • /usr/share/man/man3/TFBS::Matrix::PWM.3pm.gz
    • /usr/share/man/man3/TFBS::MatrixSet.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::AnnSpec.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::AnnSpec::Motif.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::Elph.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::Elph::Motif.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::Gibbs.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::Gibbs::Motif.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::MEME.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::MEME::Motif.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::SimplePFM.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::YMF.3pm.gz
    • /usr/share/man/man3/TFBS::PatternGen::YMF::Motif.3pm.gz
    • /usr/share/man/man3/TFBS::PatternI.3pm.gz
    • /usr/share/man/man3/TFBS::Site.3pm.gz
    • /usr/share/man/man3/TFBS::SitePair.3pm.gz
    • /usr/share/man/man3/TFBS::SitePairSet.3pm.gz
    • /usr/share/man/man3/TFBS::SiteSet.3pm.gz
    • /usr/share/man/man3/TFBS::Word.3pm.gz
    • /usr/share/man/man3/TFBS::Word::Consensus.3pm.gz

    Changelog

    2014-07-23 - Andreas Tille <tille@debian.org> libtfbs-perl (0.6.1+dfsg-1) unstable; urgency=medium * New upstream version * Moved debian/upstream to debian/upstream/metadata * Add get-orig-source target with proper uscan call * debian/watch: use uversionmangle to get properly named tarball * Add autopkgtest

    2014-01-14 - Andreas Tille <tille@debian.org> libtfbs-perl (0.6.0+dfsg-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * debian/rules: Clean up from get-orig-source since there is a real release * debian/copyright: Exclude several files which are either cruft adding useless bytes to the archive and on the other hand making the build quite complex (Makefile with broken clean target which deletes itself afterwards anyway) all those files are deleted

    2013-11-16 - Andreas Tille <tille@debian.org> libtfbs-perl (0.5.svn.20100421-2) unstable; urgency=low * debian/upstream: - Single Reference field instead of Reference-* - s/authors/author/ * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - debhelper 9 - canonical Vcs fields * debian/copyright: DEP5 * debian/rules: hardening options * debian/patches/hardening.patch: Enable building with -Wformat-security

    2011-08-25 - Charles Plessy <plessy@debian.org> libtfbs-perl (0.5.svn.20100421-1) unstable; urgency=low * New upstream SVN snapshot fixing issue related to new naming conventions. * Arranged the get-orig-source target of debian/rules to pick the date of the last upstream commit. * Corrected Vcs fields in debian/control. * Conforms with Policy 3.9.2: - Incremented Standards-Version in debian/control. - Mention GPL version 1 in debian/copyright. * Switch to Debhelper 8 and dh rules. * Converted debian/copyright to DEP-5 format.

    2009-11-28 - Charles Plessy <plessy@debian.org> libtfbs-perl (0.5.svn.20091128-1) unstable; urgency=low * New upstream SVN snapshot, adding JASPAR5 support. * Skip test that needs a network connection unless in maintainer mode. (debian/rules). Thanks to Gregor Herrmann (Closes: #533995). * Updated to Policy 3.8.3: - Incremented Standards-Version (debian/control) - Dropped version in build dependency on Perl (debian/control). - Honor the ‘nocheck’ build option (debian/rules). * Documented how this package is tested in debian/README.Debian. * Added meta-information in debian/upstream-metadata.yaml. * Refreshed debian/copyright to latest experimentations on the format. * Debhelper 7: use dh_prep and dh binary-arch in debian/rules.

    2008-08-11 - Charles Plessy <plessy@debian.org> libtfbs-perl (0.5.svn.20080722-2) unstable; urgency=low * debian/control: - Added bioperl to the build dependencies (Closes: #493341). - Dropped quilt build dependency (see below). - Added myself to the Uploaders field. - Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package. * debian/compat, debian/control: - Using debhelper 7. * debian/rules: - Refreshed with `dh-make-perl --refresh'. - Removes /usr/lib/perl5/pwm_searchPFF.c and /usr/lib/perl5/pwm_search.h, that should not be installed there. * debian/patches, debian/rules: - Disabling the MySQL tests with `echo "n" |' instead of patches. * debian/copyright: - Converted to machine-readable format. - Added myself to the Hall of Fame.

    2008-07-22 - Steffen Moeller <moeller@debian.org> libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low * Initial release (closes: #491714).

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