Package: sim4 (0.0.20121010-8)

[ Source: 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.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c, interface::commandline, Role: Program, Scope: Utility, Purpose: use::comparing, use::searching, Supports Format: Need an extra tag, works-with-format::plaintext, works-with::TODO

Other Packages Related to sim4

• dep: libc6 (>= 2.29)

  GNU C 라이브러리: 공유 라이브러리
  also a virtual package provided by libc6-udeb

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Architecture	Package Size	Installed Size	Files
amd64	350.8 kB	1,371.0 kB	[list of files]
arm64	346.8 kB	1,363.0 kB	[list of files]
armel	346.0 kB	1,362.0 kB	[list of files]
armhf	344.3 kB	1,334.0 kB	[list of files]
i386	353.0 kB	1,378.0 kB	[list of files]
mips64el	350.1 kB	1,379.0 kB	[list of files]
mipsel	349.4 kB	1,374.0 kB	[list of files]
ppc64el	356.3 kB	1,407.0 kB	[list of files]
s390x	349.9 kB	1,375.0 kB	[list of files]