sim4db_0~20150903+r2013-6_i386.deb


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Description

sim4db - batch spliced alignment of cDNA sequences to a target genome

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename sim4db_0~20150903+r2013-6_i386.deb
Package name sim4db
Package version 0~20150903+r2013
Package release 6
Package architecture i386
Package type deb
Category science
Homepage http://kmer.sourceforge.net
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 424.18 KB
Installed size 3.38 MB
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
algorithms to determine the alignments, but incorporates a fast sequence
indexing and retrieval mechanism, implemented in the sister package
'leaff', to speedily process large volumes of sequences.
While sim4db produces alignments in the same way as sim4 or sim4cc, it
has additional features to make it more amenable for use with whole-genome
annotation pipelines. A script file can be used to group pairings between
cDNAs and their corresponding genomic regions, to be aligned as one run
and using the same set of parameters. Sim4db also optionally reports more
than one alignment for the same cDNA within a genomic region, as long
as they meet user-defined criteria such as minimum length, percentage
sequence identity or coverage. This feature is instrumental in finding
all alignments of a gene family at one locus. Lastly, the output is
presented either as custom sim4db alignments or as GFF3 gene features.
This package is part of the Kmer suite.

Alternatives

Package Version Architecture Repository
sim4db_0~20150903+r2013-6_amd64.deb 0~20150903+r2013 amd64 Debian Main
sim4db - - -

Requires

Name Value
libc6 >= 2.7
libgcc1 >= 1:4.2
libstdc++6 >= 5.2

Download

Type URL
Mirror ftp.br.debian.org
Binary Package sim4db_0~20150903+r2013-6_i386.deb
Source Package kmer

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install sim4db deb package:
    # sudo apt-get install sim4db

Files

Path
/usr/bin/cleanPolishes
/usr/bin/comparePolishes
/usr/bin/convertPolishes
/usr/bin/convertToAtac
/usr/bin/convertToExtent
/usr/bin/depthOfPolishes
/usr/bin/detectChimera
/usr/bin/filterPolishes
/usr/bin/fixPolishesIID
/usr/bin/headPolishes
/usr/bin/mappedCoverage
/usr/bin/mergePolishes
/usr/bin/parseSNP
/usr/bin/pickBestPolish
/usr/bin/pickUniquePolish
/usr/bin/plotCoverageVsIdentity
/usr/bin/realignPolishes
/usr/bin/removeDuplicate
/usr/bin/reportAlignmentDifferences
/usr/bin/sim4db
/usr/bin/sortPolishes
/usr/bin/summarizePolishes
/usr/bin/uniqPolishes
/usr/bin/vennPolishes
/usr/share/doc/sim4db/README.sim4db.gz
/usr/share/doc/sim4db/README.test
/usr/share/doc/sim4db/changelog.Debian.gz
/usr/share/doc/sim4db/copyright
/usr/share/doc/sim4db/sim4db-unit-test
/usr/share/man/man1/cleanPolishes.1.gz
/usr/share/man/man1/comparePolishes.1.gz
/usr/share/man/man1/convertPolishes.1.gz
/usr/share/man/man1/convertToAtac.1.gz
/usr/share/man/man1/convertToExtent.1.gz
/usr/share/man/man1/depthOfPolishes.1.gz
/usr/share/man/man1/detectChimera.1.gz
/usr/share/man/man1/filterPolishes.1.gz
/usr/share/man/man1/fixPolishesIID.1.gz
/usr/share/man/man1/headPolishes.1.gz
/usr/share/man/man1/mappedCoverage.1.gz
/usr/share/man/man1/mergePolishes.1.gz
/usr/share/man/man1/parseSNP.1.gz
/usr/share/man/man1/pickBestPolish.1.gz
/usr/share/man/man1/pickUniquePolish.1.gz
/usr/share/man/man1/plotCoverageVsIdentity.1.gz
/usr/share/man/man1/realignPolishes.1.gz
/usr/share/man/man1/removeDuplicate.1.gz
/usr/share/man/man1/reportAlignmentDifferences.1.gz
/usr/share/man/man1/sim4db.1.gz
/usr/share/man/man1/sim4dbutils.1.gz
/usr/share/man/man1/sortPolishes.1.gz
/usr/share/man/man1/summarizePolishes.1.gz
/usr/share/man/man1/uniqPolishes.1.gz
/usr/share/man/man1/vennPolishes.1.gz

Changelog

2018-08-27 - Liubov Chuprikova <chuprikovalv@gmail.com>
kmer (0~20150903+r2013-6) unstable; urgency=medium
* Team upload.
[ Liubov Chuprikova ]
* Add autopkgtest.
* Standards-Version: 4.2.1
* Add a patch to fix wrong evaluation order in an expression
Closes: #906980
[ Andreas Tille ]
* Provide test data in new package kmer-examples to avoid duplication of
data in two packages
2018-08-26 - Andreas Tille <tille@debian.org>
kmer (0~20150903+r2013-5) unstable; urgency=medium
* Team upload
[ Adrian Bunk ]
* Use the same compile flags in all Linux builds, and include -fPIC
atac .so were built without -fPIC on !amd64/ia64.
Closes: #907007
[ Andreas Tille ]
* Standards-Version: 4.2.0
2018-08-05 - Andreas Tille <tille@debian.org>
kmer (0~20150903+r2013-4) unstable; urgency=medium
* Team upload.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Fix Perl interpreter path
* Fix spelling
2016-12-03 - Afif Elghraoui <afif@debian.org>
kmer (0~20150903+r2013-3) unstable; urgency=medium
* Rename source package to match upstream name and primary binary package
* New binary package: atac
* Drop unused packaging file for libkmer
* libkmer-dev, libmeryl-dev:
- reorganize header files and static libraries
* Remove obsolete README.Debian
* kmer: don't use Metapackages section
2016-11-28 - Afif Elghraoui <afif@debian.org>
kmer-tools (0~20150903+r2013-2) unstable; urgency=low
[ Afif Elghraoui ]
* Fix source URL in debian/copyright.
[ Andreas Tille ]
* Provide fake watch file to keep QA tools silent about no watch information
* debhelper 10
* cme fix dpkg-control
* hardening=+all
2016-01-02 - Afif Elghraoui <afif@ghraoui.name>
kmer-tools (0~20150903+r2013-1) unstable; urgency=low
* Simplify get-orig-source script
* Imported Upstream version 0~20150903+r2013
* Clean up source package: move meryl manpages to a subdirectory of debian/
* New binary packages:
- leaff
- sim4db
* Drop build-dependency on libbz2-dev
* Drop kazlib quilt patches
* Fix section/architecture of the kmer metapackage
* Set Vcs-Browser to point to cgit
* Don't install other READMEs to metapackage docs
* Update d/copyright
* Update README.source
- document situation with bundled kazlib
- document reason for monolithic source package
* Make the build system more flexible to hopefully fix build on kFreeBSD
* Add README.Debian to let users know some components aren't yet packaged
* Add comment for why we can't use dh --parallel
2015-05-01 - Afif Elghraoui <afif@ghraoui.name>
kmer-tools (0~20150520+2004-1) unstable; urgency=low
* Initial release (Closes: #784863)

See Also

Package Description
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simba_0.8.4-6_all.deb next generation mirroring tool
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simg2img_8.1.0+r23-5_all.deb Transitional package
simgrid-doc_3.21+dfsg-4_all.deb Documentation for the SimGrid Toolkit
simgrid-java_3.21+dfsg-4_i386.deb Java bindings for the SimGrid Toolkit
simh_3.8.1-6_i386.deb Emulators for 33 different computers
simhash_0.0.20150404-1+b1_i386.deb generate similarity hashes to find nearly duplicate files
similarity-tester_3.0.2-1_i386.deb Find lexical similarities between files
simple-ccsm_0.8.16-2_all.deb Simple Compizconfig settings manager
simple-cdd_0.6.7_all.deb create customized debian-installer CDs
simple-image-reducer_1.0.2-7_all.deb GTK application to easily reduce and rotate images
simple-obfs_0.0.5-5_i386.deb simple obfusacting plugin for shadowsocks-libev
simple-revision-control_1.24-1_all.deb single-file and single-user revision control system
simple-scan_3.30.1.1-1+b1_i386.deb Simple Scanning Utility
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