软件包：sim4（0.0.20121010-8）

[ 源代码： 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.

标签: 领域: 生物学, 生物信息学, 实做语言: implemented-in::c, interface::commandline, 角色: 程序, 范围: 实用程序, Purpose: use::comparing, use::searching, 支持的格式: 需要一个额外的标签, works-with-format::plaintext, works-with::TODO

其他与 sim4 有关的软件包

• dep: libc6 (>= 2.29)

  GNU C 语言运行库：共享库
  同时作为一个虚包由这些包填实： libc6-udeb

下载 sim4

下载可用于所有硬件架构的

硬件架构	软件包大小	安装后大小	文件
amd64	350.8 kB	1,371.0 kB	[文件列表]
arm64	346.8 kB	1,363.0 kB	[文件列表]
armel	346.0 kB	1,362.0 kB	[文件列表]
armhf	344.3 kB	1,334.0 kB	[文件列表]
i386	353.0 kB	1,378.0 kB	[文件列表]
mips64el	350.1 kB	1,379.0 kB	[文件列表]
mipsel	349.4 kB	1,374.0 kB	[文件列表]
ppc64el	356.3 kB	1,407.0 kB	[文件列表]
s390x	349.9 kB	1,375.0 kB	[文件列表]