sim4 binary package in Ubuntu Trusty i386

 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.

Publishing history

Date Status Target Pocket Component Section Priority Phased updates Version
  2013-10-24 17:32:13 UTC Published Ubuntu Trusty i386 release universe science Optional 0.0.20121010-1
  • Published
  • Copied from ubuntu trusty-proposed i386 in Primary Archive for Ubuntu
  Deleted Ubuntu Trusty i386 proposed universe science Optional 0.0.20121010-1
  • Removal requested .
  • Deleted by Ubuntu Archive Robot

    moved to release

  • Published
  2013-10-24 17:35:58 UTC Superseded Ubuntu Trusty i386 release universe science Optional 0.0.20030921-3
  • Removal requested .
  • Superseded by i386 build of sim4 0.0.20121010-1 in ubuntu trusty PROPOSED
  • Published
  • Copied from ubuntu intrepid-release i386 in Primary Archive for Ubuntu

Source package