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[ Source: sim4  ]

Package: sim4 (0.0.20030921-3)

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: C, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Comparing, Searching, Supports Format: Plain Text

Other Packages Related to sim4

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  • dep: libc0.1 (>= 2.3) [kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.7-1) [hurd-i386]
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    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.5) [avr32]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.5-5) [m68k]
    dep: libc6 (>= 2.7-1) [not alpha, avr32, hurd-i386, ia64, kfreebsd-amd64, kfreebsd-i386, m68k]
  • dep: libc6.1 (>= 2.7-1) [alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb

Download sim4

Download for all available architectures
Architecture Package Size Installed Size Files
alpha 59.0 kB164 kB [list of files]
amd64 53.4 kB144 kB [list of files]
armel 52.8 kB140 kB [list of files]
avr32 (unofficial port) 56.0 kB124 kB [list of files]
hppa 53.9 kB140 kB [list of files]
hurd-i386 47.8 kB132 kB [list of files]
i386 48.8 kB132 kB [list of files]
ia64 75.8 kB220 kB [list of files]
kfreebsd-amd64 54.1 kB122 kB [list of files]
kfreebsd-i386 49.1 kB110 kB [list of files]
m68k (unofficial port) 42.4 kB124 kB [list of files]
mips 55.2 kB160 kB [list of files]
mipsel 55.9 kB164 kB [list of files]
powerpc 53.5 kB144 kB [list of files]
s390 51.4 kB140 kB [list of files]
sparc 49.2 kB136 kB [list of files]