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[ Source: epcr  ]

Package: ncbi-epcr (2.3.10-1 and others)

Tool to test a DNA sequence for the presence of sequence tagged sites

Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.

The new version of e-PCR implements a fuzzy matching strategy. To reduce likelihood that a true STS will be missed due to mismatches, multiple discontigous words may be used instead of a single exact word. Each of this word has groups of significant positions separated by 'wildcard' positions that are not required to match. In addition, it is also possible to allow gaps in the primer alignments.

The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database.

Tags: Field: Biology, Role: Program, Scope: Utility

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  • dep: libc0.1 (>= 2.7-1) [kfreebsd-amd64, kfreebsd-i386]
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    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.3.5-1) [hurd-i386]
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  • dep: libc6 (>= 2.5-5) [m68k]
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  • dep: libc6.1 (>= 2.7-1) [alpha, ia64]
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  • dep: libgcc1 (>= 1:4.1.1-12) [hurd-i386]
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    dep: libgcc1 (>= 1:4.1.1-21) [alpha, amd64, i386, ia64]
    dep: libgcc1 (>= 1:4.2.1-4) [mips, mipsel, powerpc, s390, sparc]
    dep: libgcc1 (>= 1:4.3) [arm, armel, kfreebsd-amd64, kfreebsd-i386]
  • dep: libgcc2 (>= 4.2.1-1) [m68k]
    GCC support library
  • dep: libgcc4 (>= 4.1.1-21) [hppa]
    GCC support library
  • dep: libstdc++6 (>= 4.1.1-12) [hurd-i386]
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    dep: libstdc++6 (>= 4.2.1-4) [not armel, hurd-i386, kfreebsd-amd64, kfreebsd-i386]
    dep: libstdc++6 (>= 4.3) [armel, kfreebsd-amd64, kfreebsd-i386]
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Download ncbi-epcr

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha 2.3.10-1 211.0 kB640 kB [list of files]
amd64 2.3.10-1 195.2 kB520 kB [list of files]
arm 2.3.10-1 219.1 kB548 kB [list of files]
armel 2.3.10-1 183.8 kB472 kB [list of files]
hppa 2.3.10-1 231.9 kB584 kB [list of files]
hurd-i386 1.2.0-3 14.4 kB76 kB [list of files]
i386 2.3.10-1 188.5 kB476 kB [list of files]
ia64 2.3.10-1 268.8 kB892 kB [list of files]
kfreebsd-amd64 (unofficial port) 2.3.10-1 196.4 kB464 kB [list of files]
kfreebsd-i386 (unofficial port) 2.3.10-1 191.8 kB432 kB [list of files]
m68k 2.3.10-1 177.9 kB484 kB [list of files]
mips 2.3.10-1 209.7 kB692 kB [list of files]
mipsel 2.3.10-1 209.8 kB692 kB [list of files]
powerpc 2.3.10-1 204.6 kB544 kB [list of files]
s390 2.3.10-1 192.1 kB504 kB [list of files]
sparc 2.3.10-1 196.9 kB528 kB [list of files]