Filewatcher File Search File Search
Catalog
Content Search
» » » » »

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:2.3.12-1-1
Architecture:sparc
Distribution:Debian
Filename:ncbi-epcr_2.3.12-1-1_sparc.deb

/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 sequence tagged sites (STS) in DNA sequences

SYNOPSIS
       e-PCR  [-hV]  [posix-options]  stsfile  [fasta  ...] [compat-
       options]

DESCRIPTION
       The program  substitutes  blast  in  the  location  of  pairs
       primers on the genome that may yield a PCR product.


OPTIONS
       pos
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 (2.3.12-1-1) unstable; urgency=low

  * New upstream version that has applied debian/patches/gc
more»

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

version		 2.3.12
affected:	 few *.cpp files
description:
	- Added include of cstdio to make it compi
more»

Browse inside ncbi-epcr_2.3.12-1-1_sparc.deb

         [DIR]DEBIAN/ (2)  65535+ mirrors
         [DIR]usr/ (2)  65535+ mirrors

Download ncbi-epcr_2.3.12-1-1_sparc.deb

Results 1 - 1 of 1
Help - FTP Sites List - Software Dir.
Search over 15 billion files
© 1997-2016 FileWatcher.com