sim4 - tool for aligning cDNA and genomic DNA

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: sim4
Package version: 0.0.20121010
Package release: 2
Package architecture: i386
Package type: deb
Installed size: 111 B
Download size: 48.53 KB
Official Mirror:
sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other). sim4 employs a blast-based technique to first determine the basic matching blocks representing the "exon cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.




    Source package: sim4

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install sim4 deb package:
      # sudo apt-get install sim4


    • /usr/bin/sim4
    • /usr/share/doc/sim4/changelog.Debian.gz
    • /usr/share/doc/sim4/copyright
    • /usr/share/man/man1/sim4.1.gz


    2016-01-21 - Andreas Tille <> sim4 (0.0.20121010-2) unstable; urgency=medium * Moved debian/upstream to debian/upstream/metadata * More precise homepage * cme fix dpkg-control * DEP5 names

    2013-08-02 - Andreas Tille <> sim4 (0.0.20121010-1) unstable; urgency=low * New upstream version * debian/upstream: add citation information * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - debhelper 9 - drop cdbs build-depends - anonscm in Vcs fields * debian/rules: short dh * debian/patches/hardening.patch: propagate hardening options * debian/copyright: DEP5

    2008-03-18 - Andreas Tille <> sim4 (0.0.20030921-3) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description. [ David Paleino ] * Updated to Standards-Version 3.7.3 (no changes needed) [ Andreas Tille ] * Added myself to Uploaders

    2007-08-15 - Nelson A. de Oliveira <> sim4 (0.0.20030921-2) unstable; urgency=low * Updated patches/Makefile.diff, so sim4 doesn't get stripped when using DEB_BUILD_OPTIONS=nostrip (Closes: #438021); * Changed maintainer to Debian-Med Packaging Team <>; * Added SVN repository URL in debian/control; * Updated my email address; * Updated Standards-Version to 3.7.2; * Updated debhelper compatibility level to 5; * Updated FSF address in copyright file; * Updated watch file.

    2005-08-03 - Nelson A. de Oliveira <> sim4 (0.0.20030921-1) unstable; urgency=low * Initial release. (Closes: #321180)