e-pcr(1) [debian man page]
E-PCR(1) General Commands Manual 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
posix-options are: -m=## Margin (default 50) -w=## Wordsize (default 7) -n=## Max mismatches allowed (default 0) -g=## Max indels allowed (default 0) -f=## Use ## disontiguous words, slow if ##>1 -o=## Set output file -t=## Set output format: 1 - classic, range (pos1..pos2) 2 - classic, midpoint 3 - tabular 4 - tabular with alignment in comments (slow) -d=##-## Set default size range (default 100-350) -p=+- Turn hits postprocess on/off -v=## Verbosity flags -a=a|f Use presize alignments (only if gaps>0), slow a - Always or f - as Fallback -x=+- Use 5'-end lowercase masking of primers (default -) -u=+- Uppercase all primers (default -) compat-options (duplicate posix-options) are M=## Margin (default 50) W=## Wordsize (default 7) N=## Number of mismatches allowed (default 0) G=## Max indels allowed (default 0) F=## Use ## discontinuous words O=## Set output file to ## T=## Set output format (1..3) D=##-## Set default size range P=+- Postprocess hits on/off V=## Verbosity flags A=a|f Use presize alignments (only if gaps>0), slow a - Always or f - as Fallback X=+- Use 5'-end lowercase masking of primers (default -) U=+- Uppercase all primers (default -) -mid Same as T=2 For information about further options just call e-PCR without any options. SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt bioperl(1), re-pcr(1) AUTHORS
This manual page was written by Steffen Moeller <moeller@debian.org> and Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. February 2004 E-PCR(1)
Check Out this Related Man Page
Bio::PrimerDesigner::epcr(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::epcr(3pm) NAME
Bio::PrimerDesigner::epcr - A class for accessing the epcr binary SYNOPSIS
use Bio::PrimerDesigner::epcr; DESCRIPTION
A low-level interface to the e-PCR binary. Uses supplied PCR primers, DNA sequence and stringency parameters to predict both expected and unexpected PCR products. METHODS
run Sets up the e-PCR request for a single primer combination and returns an Bio::PrimerDesigner::Result object If the permute flag is true, all three possible primer combinations will be tested (ie: forward + reverse, forward + forward, reverse + reverse) request Assembles the e-PCR config file and command-line arguments and send the e-PCR request to the local e-PCR binary or remote server. verify Check to make that the e-PCR binary is installed and functioning properly. Since e-PCR returns nothing if no PCR product is found in the sequence, we have to be able to distinguish between a valid, undefined output from a functioning e-PCR and an undefined output for some other reason. verify uses sham e-PCR data that is known to produce a PCR product. binary_name Defines the binary's name on the system. list_aliases There are no aliases to list for epcr. list_params Returns a list of e-PCR configuration options. Required e-PCR input is a sequence string or file and the left and right primers. Default values will be used for the remaining options if none are supplied. AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>. LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. SEE ALSO
Bio::PrimerDesigner::primer3. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::epcr(3pm)