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

Distribution: Ubuntu 12.04 LTS (Precise Pangolin)
Repository: Ubuntu Universe amd64
Package name: ncbi-epcr
Package version: 2.3.12
Package release: 2
Package architecture: amd64
Package type: deb
Installed size: 756 B
Download size: 223.04 KB
Official Mirror:
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.



    Source package: epcr

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install ncbi-epcr deb package:
      # sudo apt-get install ncbi-epcr


    • /usr/bin/e-PCR
    • /usr/bin/fahash
    • /usr/bin/famap
    • /usr/bin/re-PCR
    • /usr/share/doc/ncbi-epcr/README.Debian
    • /usr/share/doc/ncbi-epcr/README.html
    • /usr/share/doc/ncbi-epcr/README.txt.gz
    • /usr/share/doc/ncbi-epcr/changelog.Debian.gz
    • /usr/share/doc/ncbi-epcr/copyright
    • /usr/share/man/man1/e-PCR.1.gz
    • /usr/share/man/man1/fahash.1.gz
    • /usr/share/man/man1/famap.1.gz
    • /usr/share/man/man1/re-PCR.1.gz