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[ Source: sim4  ]

Package: sim4 (0.0.20121010-4)

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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

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Download sim4

Download for all available architectures
Architecture Package Size Installed Size Files
alpha (unofficial port) 390.2 kB473.0 kB [list of files]
amd64 386.7 kB449.0 kB [list of files]
arm64 380.0 kB440.0 kB [list of files]
armel 381.8 kB448.0 kB [list of files]
armhf 380.3 kB420.0 kB [list of files]
hppa (unofficial port) 383.9 kB444.0 kB [list of files]
hurd-i386 386.2 kB452.0 kB [list of files]
i386 388.2 kB456.0 kB [list of files]
kfreebsd-amd64 386.2 kB449.0 kB [list of files]
kfreebsd-i386 385.8 kB448.0 kB [list of files]
m68k (unofficial port) 375.7 kB432.0 kB [list of files]
mips 384.9 kB460.0 kB [list of files]
mips64el 386.0 kB466.0 kB [list of files]
mipsel 385.2 kB460.0 kB [list of files]
powerpc 382.8 kB488.0 kB [list of files]
powerpcspe (unofficial port) 382.6 kB488.0 kB [list of files]
ppc64 (unofficial port) 385.3 kB490.0 kB [list of files]
ppc64el 385.8 kB488.0 kB [list of files]
s390x 386.9 kB464.0 kB [list of files]
sh4 (unofficial port) 385.3 kB428.0 kB [list of files]
sparc64 (unofficial port) 381.4 kB450.0 kB [list of files]
x32 (unofficial port) 385.8 kB448.0 kB [list of files]