re-pcr(1) [debian man page]

RE-PCR(1)						      General Commands Manual							 RE-PCR(1)

NAME

       re-PCR -- Find sequence tagged sites (STS) in DNA sequences

SYNOPSIS

       re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]

       re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]

       re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]

       re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]

DESCRIPTION

       Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by per-
       forming STS and primer searches.

OPTIONS

       -p=hash-file
		 Perform primer lookup using hash-file

       -P=hash-file
		 Perform primer lookup using hash-file

       -s=hash-file
		 Perform STS lookup using hash-file

       -S=hash-file
		 Perform STS lookup using hash-file

       -n=mism	 Set max allowed mismatches per primer for lookup

       -g=gaps	 Set max allowed indels per primer for lookup

       -m=margin Set variability for STS size for lookup

       -l	 Use presize alignments (only if gaps>0)

       -G	 Print alignments in comments

       -d=min-max
		 Set default STS size

       -r=+|-	 Enable/disable reverse STS lookup

       -O=+|-	 Enable/disable syscall optimisation

       -C=batchcnt
		 Set number of STSes per batch

       -o=outfile
		 Set output file name

       -q	 Quiet (no progress indicator)

EXAMPLE

	famap -tN -b genome.famap org/chr_*.fa

	fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

	re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

       See famap(1) and fahash(1)

SEE ALSO

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

       bioperl(1), e-pcr(1), famap(1) and fahash(1)

AUTHORS

       This manual page was written by 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.

								    April 2008								 RE-PCR(1)

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)