Paket: sim4 (0.0.20121010-5)

[ Kaynak: sim4  ]

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.

Etiketler: Alan: Biyoloji, Biyoinformatik, Geliştirildiği dil: implemented-in::c, interface::commandline, Rol: Program, Kapsam: Yardımcı Araç, Amaç: use::comparing, use::searching, Desteklenen Biçimler: Ek etiket gerektiriyor, works-with-format::plaintext, works-with::TODO

sim4 ile İlgili Diğer Paketler

• dep: libc6 (>= 2.14)

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb

sim4 indir

Tüm mevcut mimariler için indir

Mimari	Paket Boyutu	Kurulu Boyut	Dosyalar
amd64	387,0 kB	453,0 kB	[dosya listesi]