sim4 - tool for aligning cDNA and genomic DNA

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename sim4_0.0.20121010-5_i386.deb
Package name sim4
Package version 0.0.20121010
Package release 5
Package architecture i386
Package type deb
Category field::biology field::biology:bioinformatics implemented-in::c interface::commandline role::program science scope::utility use::comparing use::searching works-with-format::TODO works-with-format::plaintext works-with::TODO
License -
Maintainer Debian Med Packaging Team <>
Download size 387.64 KB
Installed size 460.00 KB
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.


Package Version Architecture Repository
sim4_0.0.20121010-5_amd64.deb 0.0.20121010 amd64 Debian Main
sim4 - - -


Name Value
libc6 >= 2.7


Type URL
Binary Package sim4_0.0.20121010-5_i386.deb
Source Package sim4

Install Howto

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




2018-07-17 - Andreas Tille <>
sim4 (0.0.20121010-5) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to
* Standards-Version: 4.1.5
2016-10-27 - Canberk Koç <>
sim4 (0.0.20121010-4) unstable; urgency=medium
[ Canberk Koç ]
* Team upload.
* Autopkgtests added
* README.source file added 
2016-04-12 - Andreas Tille <>
sim4 (0.0.20121010-3) unstable; urgency=medium
[ Andreas Tille ]
* Moved packaging to Git
[ Alexis Bienvenüe ]
* Sort c files for reproducible build
Closes: #820741
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)

See Also

Package Description
sim4db_0~20150903+r2013-6_i386.deb batch spliced alignment of cDNA sequences to a target genome
simavr_1.6+dfsg-1_i386.deb lean and mean AVR simulator
simba_0.8.4-6_all.deb next generation mirroring tool
simbody-doc_3.6.1+dfsg-7_all.deb SimTK multibody dynamics API - Documentation
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