libtfbs-perl_0.7.1-2+b1_i386.deb


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Description

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

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename libtfbs-perl_0.7.1-2+b1_i386.deb
Package name libtfbs-perl
Package version 0.7.1
Package release 2+b1
Package architecture i386
Package type deb
Category devel::lang:perl devel::library field::biology field::biology:bioinformatics implemented-in::c implemented-in::perl interface::commandline perl role::devel-lib role::program
Homepage http://tfbs.genereg.net
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 237.51 KB
Installed size 838.00 KB
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".
Note: the TFBS perl module is no longer under active development.  All the
functionality can be found in the TFBSTools Bioconductor package; users are
highly encouraged to switch.  <http://bioconductor.org/packages/TFBSTools/>

Alternatives

Package Version Architecture Repository
libtfbs-perl_0.7.1-2+b1_amd64.deb 0.7.1 amd64 Debian Main
libtfbs-perl - - -

Requires

Name Value
bioperl -
libc6 >= 2.4
libdbi-perl -
libwww-perl -
pdl >= 1:2.019-5+b1
pdlapi-12 -
perl >= 5.28.0-3
perlapi-5.28.0 -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package libtfbs-perl_0.7.1-2+b1_i386.deb
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

Path
/usr/lib/i386-linux-gnu/perl5/5.28/pwm_search.h
/usr/lib/i386-linux-gnu/perl5/5.28/pwm_searchPFF.c
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/ConservationProfile.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/MatrixSet.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGenI.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternI.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/README.md
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Site.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/SitePair.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/SitePairSet.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/SiteSet.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/TFFM.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Word.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/_Iterator.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/FlatFileDir.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR2.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR4.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR5.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR6.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/JASPAR7.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/LocalTRANSFAC.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/DB/TRANSFAC.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Ext/pwmsearch.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix/Alignment.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix/ICM.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix/PFM.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix/PWM.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Matrix/_Alignment.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/AnnSpec.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Elph.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Gibbs.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/MEME.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/SimplePFM.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/YMF.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/AnnSpec/Motif.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Elph/Motif.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Gibbs/Motif.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/MEME/Motif.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Motif/Matrix.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/Motif/Word.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/PatternGen/YMF/Motif.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Run/ConservationProfileGenerator.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Tools/SetOperations.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/Word/Consensus.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/_Iterator/_MatrixSetIterator.pm
/usr/lib/i386-linux-gnu/perl5/5.28/TFBS/_Iterator/_SiteSetIterator.pm
/usr/lib/i386-linux-gnu/perl5/5.28/auto/TFBS/Ext/pwmsearch/pwmsearch.bundle
/usr/lib/i386-linux-gnu/perl5/5.28/auto/TFBS/Ext/pwmsearch/pwmsearch.so
/usr/share/doc/libtfbs-perl/README.Debian
/usr/share/doc/libtfbs-perl/changelog.Debian.gz
/usr/share/doc/libtfbs-perl/changelog.Debian.i386.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::JASPAR.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::JASPAR7.3pm.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::TFFM.3pm.gz
/usr/share/man/man3/TFBS::Word.3pm.gz
/usr/share/man/man3/TFBS::Word::Consensus.3pm.gz

Changelog

2018-10-16 - Andreas Tille <tille@debian.org>
libtfbs-perl (0.7.1-2) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove redundant get-orig-source target
* Fix permissions
* Drop obsolete needs-recommends from debian/tests/control and add
recommended libgd-gd2-perl to Depends
* Drop unneeded Testsuite: autopkgtest
* Fix perl interpreter path
* Do not parse d/changelog
2017-10-21 - Charles Plessy <plessy@debian.org>
libtfbs-perl (0.7.1-1) unstable; urgency=medium
* New upstream version 0.7.1
* d/copyright, d/watch: Stop repacking upstream sources.
* d/control:
- Add upstream's notice of deprecation to the package's description.
- Remove cruft Makefiles at build time.
- Conforms to Policy version 4.1.1.
2016-12-17 - Andreas Tille <tille@debian.org>
libtfbs-perl (0.7.0+dfsg-4) unstable; urgency=medium
* d/watch: version=4
* debhelper 10
2016-07-16 - Tatiana Malygina <merlettaia@gmail.com>
libtfbs-perl (0.7.0+dfsg-3) unstable; urgency=medium
* Team upload.
* add tests (except smoke tests - since debian/tests/run-unit-tests does the
same thing as they do) from autopkgtest-pkg-perl to debian/tests/control.
For more details see this page (and link to default-tests-control file):
https://pkg-perl.alioth.debian.org/autopkgtest.html#implementation
2016-07-12 - Andreas Tille <tille@debian.org>
libtfbs-perl (0.7.0+dfsg-2) unstable; urgency=medium
* Moved packaging from SVN to Git
* NMU Closes: #827499
2016-06-24 - Bas Couwenberg <sebastic@debian.org>
libtfbs-perl (0.7.0+dfsg-1.1) unstable; urgency=medium
* Non-maintainer upload.
* Use dh_pdl to set versioned pdl dependency via ${pdl:Depends}.
* Update Vcs-Browser URL to use HTTPS.
* Update watch file to handle common issues.
* Enable all hardening buildflags, except PIE (causes build failure).
* Bump Standards-Version to 3.9.8, no changes.
* Add patch to fix spelling errors.
* Require at least pdl 2.016 for pdl transition.
2015-11-08 - Andreas Tille <tille@debian.org>
libtfbs-perl (0.7.0+dfsg-1) unstable; urgency=medium
* New upstream version
* cme fix dpkg-control
* fixed watch file
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

See Also

Package Description
libtfm-dev_0.13-4_i386.deb Fast multiple-precision integer library [development files]
libtfm1_0.13-4_i386.deb Fast multiple-precision integer library [runtime]
libtgl-0.0.0.20160623-0_2.0.1+git20160323.ffb04cac-3_i386.deb telegram API library
libtgl-0.0.0.20160623-dev_2.0.1+git20160323.ffb04cac-3_i386.deb telegram API library (development headers)
libtgvoip-dev_2.4.2-1_i386.deb VoIP library for Telegram clients - developer files
libthai-data_0.1.28-2_all.deb Data files for Thai language support library
libthai-dev_0.1.28-2_i386.deb Development files for Thai language support library
libthai-doc_0.1.28-2_all.deb Documentation files for Thai language support library
libthai0_0.1.28-2_i386.deb Thai language support library
libthemedsupport_1.1.15-1_i386.deb Theme-D support library
libtheora-bin_1.1.1+dfsg.1-15_i386.deb Theora Video Compression Codec (example encoder, decoder)
libtheora-dev_1.1.1+dfsg.1-15_i386.deb Theora Video Compression Codec (development files)
libtheora-doc_1.1.1+dfsg.1-15_all.deb Theora Video Compression Codec (documentation)
libtheora-ocaml-dev_0.3.1-2_i386.deb OCaml interface to the theora library
libtheora-ocaml_0.3.1-2_i386.deb OCaml interface to the theora library
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