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ncbi-epcr

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

Variants:
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.

Homepage:
Package version:2.3.12-1
Architecture:armel
Distribution:Debian
Filename:ncbi-epcr_2.3.12-1_armel.deb

/usr/share/doc/ncbi-epcr/README.Debian

e-pcr for Debian
----------------

As a scientist please remember to cite 
	Gregory D. Schuler
	Sequence Mapping by Electronic PCR
	Genome Research 7:541-550
when using this program and consider to inform the author at
schuler@ncbi.nlm.nih.gov on such citations.

 -- Steffen Moeller <moeller@debian.org>, Thu, 20 Nov 2003 12:50:19 +0100

/usr/share/doc/ncbi-epcr/README.html

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Electronic PCR commandline tools: operating instructions</title>
<meta name="
            author
          " content="Greg Schuler, NCBI
              ;
            Kirill Rotmistrovsky, NCBI
              ;
            ">
<style>
          body {
          }
          hr.section-sep {
            width: 100% 
more»

/usr/share/doc/ncbi-epcr/README.txt.gz

           Electronic PCR commandline tools: operating instructions

                                                          Version: 2.3.12
     _________________________________________________________________

   Use e-PCR to map sequences using STS database

   Use re-PCR to map STSes or short primers in sequence database

   Use famap and fahash to prepare sequence database for re-PCR sear
more»

/usr/share/man/man1/e-PCR.1.gz

E-PCR(1)                                                    E-PCR(1)



NAME
       e-PCR — Find s
more»

/usr/share/man/man1/fahash.1.gz

FAHASH(1)                   User Commands                  FAHASH(1)



NAME
       fahash - sequenc
more»

/usr/share/man/man1/famap.1.gz

FASTA(1)                    User Commands                   FASTA(1)



NAME
       famap - prepare 
more»

/usr/share/man/man1/re-PCR.1.gz

RE-PCR(1)                                                  RE-PCR(1)



NAME
       re-PCR — Find 
more»

/usr/share/doc/ncbi-epcr/changelog.Debian.gz

epcr (2.3.12-1) unstable; urgency=low

  * New upstream release buildable with GCC 4.4 (Closes: #504
more»

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