sim4db_0~20150903+r2013-1_i386.deb


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Description

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

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name sim4db
Package version 0~20150903+r2013
Package release 1
Package architecture i386
Package type deb
Installed size 3.27 KB
Download size 412.18 KB
Official Mirror archive.ubuntu.com
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+r2013-1_amd64.deb 0~20150903+r2013 amd64 Ubuntu Universe
sim4db - - -

Requires

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

Download

Type URL
Binary Package sim4db_0~20150903+r2013-1_i386.deb
Source Package kmer-tools

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/changelog.Debian.gz
/usr/share/doc/sim4db/copyright
/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

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
simba_0.8.4-4.2_all.deb next generation mirroring tool
simbody-doc_3.5.3+dfsg-1ubuntu1_all.deb SimTK multibody dynamics API - Documentation
simgrid-doc_3.11.1-10ubuntu1_all.deb Documentation for the SimGrid Toolkit
simgrid-java_3.11.1-10ubuntu1_i386.deb Java bindings for the SimGrid Toolkit
simh_3.8.1-5build1_i386.deb Emulators for 33 different computers
simhash_0.0.20110213-1_i386.deb generate similarity hashes to find nearly duplicate files
similarity-tester_2.89-1_i386.deb Find lexical similarities between files
simon-data_0.4.1-0ubuntu9_all.deb open-source speech recognition program - data files
simon_0.4.1-0ubuntu9_i386.deb open-source speech recognition program
simple-cdd_0.6.1_all.deb create customized debian-installer CDs
simple-image-reducer_1.0.2-3_all.deb GTK application to easily reduce and rotate images
simple-tpm-pk11_0.04-1_i386.deb simple library for using the TPM chip to secure SSH keys
simple_0.11.1-1_i386.deb minimalist web framework for the WAI server interface
simplebackup_0.1.6-0ubuntu1_all.deb Simple backup tool
simpleburn_1.7.3-1_i386.deb Minimalistic application for burning and extracting CDs and DVDs
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