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[ Source: sim4  ]

Package: sim4 (0.0.20121010-1)

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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) 62.7 kB122.0 kB [list of files]
amd64 48.6 kB133.0 kB [list of files]
arm64 (unofficial port) 43.0 kB125.0 kB [list of files]
armel 53.1 kB128.0 kB [list of files]
armhf 46.5 kB100.0 kB [list of files]
hppa (unofficial port) 45.8 kB129.0 kB [list of files]
hurd-i386 50.6 kB128.0 kB [list of files]
i386 50.6 kB128.0 kB [list of files]
kfreebsd-amd64 54.3 kB102.0 kB [list of files]
kfreebsd-i386 50.5 kB97.0 kB [list of files]
m68k (unofficial port) 38.5 kB80.0 kB [list of files]
mips 55.8 kB144.0 kB [list of files]
mipsel 56.3 kB144.0 kB [list of files]
powerpc 52.9 kB128.0 kB [list of files]
powerpcspe (unofficial port) 44.1 kB128.0 kB [list of files]
ppc64 (unofficial port) 46.9 kB144.0 kB [list of files]
s390x 58.2 kB145.0 kB [list of files]
sh4 (unofficial port) 52.8 kB120.0 kB [list of files]
sparc 49.6 kB124.0 kB [list of files]
sparc64 (unofficial port) 56.2 kB135.0 kB [list of files]
x32 (unofficial port) 48.3 kB132.0 kB [list of files]