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[ Source: sim4  ]

Package: sim4 (0.0.20030921-3) [universe]

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Maintainer:

Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

  • Debian-Med Packaging Team (Mail Archive)
  • Nelson A. de Oliveira
  • Andreas Tille

It should generally not be necessary for users to contact the original maintainer.

External Resources:

Similar packages:

tool for aligning cDNA and genomic DNA

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.

Other Packages Related to sim4

  • depends
  • recommends
  • suggests
  • enhances
  • dep: libc6 (>= 2.4)
    Embedded GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb

Download sim4

Download for all available architectures
Architecture Package Size Installed Size Files
i386 49.8 kB136.0 kB [list of files]