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[ Source: epcr  ]

Package: ncbi-epcr (2.3.12-1 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, 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: 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 (>= 2.3.5-1) [hurd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.2) [hppa, i386, mips, mipsel]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.2.5) [amd64]
    dep: libc6 (>= 2.4) [armel, powerpc, s390]
    dep: libc6 (>= 2.5) [avr32]
    dep: libc6 (>= 2.5-5) [m68k]
    dep: libc6 (>= 2.6) [sparc]
  • dep: libc6.1 (>= 2.2) [ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
    dep: libc6.1 (>= 2.4) [alpha]
  • dep: libgcc1 (>= 1:4.1.1) [alpha, amd64, i386, ia64]
    GCC support library
    dep: libgcc1 (>= 1:4.1.1-12) [hurd-i386]
    dep: libgcc1 (>= 1:4.2.1) [avr32, mips, mipsel, powerpc, s390, sparc]
    dep: libgcc1 (>= 1:4.3.0) [armel]
    dep: libgcc1 (>= 1:4.4) [kfreebsd-amd64, kfreebsd-i386]
  • dep: libgcc2 (>= 4.2.1) [m68k]
    Package not available
  • dep: libgcc4 (>= 4.1.1) [hppa]
    GCC support library
  • dep: libstdc++6 (>= 4.1.1-12) [hurd-i386]
    The GNU Standard C++ Library v3
    dep: libstdc++6 (>= 4.2.1) [not armel, hurd-i386, kfreebsd-amd64, kfreebsd-i386]
    dep: libstdc++6 (>= 4.4) [kfreebsd-amd64, kfreebsd-i386]
    dep: libstdc++6 (>= 4.4.0) [armel]
  • dep: libunwind7 (>= 0.98.5-6) [ia64]
    A library to determine the call-chain of a program - runtime
  • rec: bioperl
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  • rec: ncbi-epcr-data
    Package not available
  • sug: bioperl
    Perl tools for computational molecular biology

Download ncbi-epcr

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha 2.3.12-1 213.9 kB640 kB [list of files]
amd64 2.3.12-1 194.5 kB520 kB [list of files]
armel 2.3.12-1 183.7 kB472 kB [list of files]
avr32 (unofficial port) 2.3.12-1 226.2 kB520 kB [list of files]
hppa 2.3.12-1 231.7 kB584 kB [list of files]
hurd-i386 1.2.0-3 14.4 kB76 kB [list of files]
i386 2.3.12-1 187.9 kB476 kB [list of files]
ia64 2.3.12-1 268.8 kB892 kB [list of files]
kfreebsd-amd64 2.3.12-1 194.6 kB462 kB [list of files]
kfreebsd-i386 2.3.12-1 187.7 kB426 kB [list of files]
m68k (unofficial port) 2.3.12-1 177.3 kB484 kB [list of files]
mips 2.3.12-1 200.9 kB668 kB [list of files]
mipsel 2.3.12-1 200.9 kB668 kB [list of files]
powerpc 2.3.12-1 201.6 kB544 kB [list of files]
s390 2.3.12-1 191.6 kB504 kB [list of files]
sparc 2.3.12-1 196.8 kB528 kB [list of files]