Package: ncbi-epcr (2.3.12-1-9)

[ Source: epcr  ]

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 discontiguous 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.

This program is retired upstream and it is suggested to use Primer-Blast

 https://www.ncbi.nlm.nih.gov/tools/primer-blast/

instead.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c++, interface::commandline, Role: Program, Scope: Utility, Purpose: use::checking, use::searching, Supports Format: Plain Text, Works with: Need an extra tag

Other Packages Related to ncbi-epcr

• dep: libc6 (>= 2.14) [amd64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.17) [arm64, ppc64el]

  dep: libc6 (>= 2.4) [not amd64, arm64, ppc64el]

• dep: libgcc-s1 (>= 3.0) [amd64, s390x]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [arm64, i386, mips64el, ppc64el]

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• sug: bioperl

  Perl tools for computational molecular biology

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amd64	164.4 kB	496.0 kB	[list of files]
arm64	153.9 kB	460.0 kB	[list of files]
armel	143.5 kB	416.0 kB	[list of files]
armhf	144.3 kB	332.0 kB	[list of files]
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mips64el	162.7 kB	594.0 kB	[list of files]
ppc64el	167.9 kB	692.0 kB	[list of files]
s390x	153.5 kB	496.0 kB	[list of files]