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E-PCR

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E-pcr

http://www.ncbi.nlm.nih.gov/sutils/e-pcr/
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.


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Licensing

LicenseVerified byVerified onNotes
PublicDomainDebian20 March 2013
GPLv2orlaterDebian20 March 2013



Leaders and contributors

Contact(s)Role
"Email rotmistr@ncbi.nlm.nih.gov" Kirill Rotmistrovsky contact


Resources and communication

Audience Resource type URI
Download ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-2.3.12-src.tar.gz


Software prerequisites



Entry



Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/epcr

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Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.


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