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[ Source: epcr  ]

Package: ncbi-epcr (2.3.10-1)

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, Bioinformatics, Implemented in: C++, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Checking, Searching, Supports Format: Plain Text

Other Packages Related to ncbi-epcr

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.7-1) [not alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libc6.1 (>= 2.7-1) [alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
  • dep: libgcc1 (>= 1:4.1.1-21) [alpha, amd64, i386, ia64]
    GCC support library
    dep: libgcc1 (>= 1:4.2.1-4) [mips, mipsel, powerpc, s390, sparc]
    dep: libgcc1 (>= 1:4.3) [arm, armel]
  • dep: libgcc4 (>= 4.1.1-21) [hppa]
    GCC support library
  • dep: libstdc++6 (>= 4.2.1-4) [not armel]
    The GNU Standard C++ Library v3
    dep: libstdc++6 (>= 4.3) [armel]
  • dep: libunwind7 (>= 0.98.5-6) [ia64]
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  • sug: bioperl
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Download ncbi-epcr

Download for all available architectures
Architecture Package Size Installed Size Files
alpha 211.0 kB640 kB [list of files]
amd64 195.2 kB520 kB [list of files]
arm 219.1 kB548 kB [list of files]
armel 183.8 kB472 kB [list of files]
hppa 231.9 kB584 kB [list of files]
i386 188.5 kB476 kB [list of files]
ia64 268.8 kB892 kB [list of files]
mips 209.7 kB692 kB [list of files]
mipsel 209.8 kB692 kB [list of files]
powerpc 204.6 kB544 kB [list of files]
s390 192.1 kB504 kB [list of files]
sparc 196.9 kB528 kB [list of files]