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

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:
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.



    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


    • /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


    2016-01-02 - Afif Elghraoui <> 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 <> kmer-tools (0~20150520+2004-1) unstable; urgency=low * Initial release (Closes: #784863)