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primer3_core(1) [debian man page]

PRIMER3_CORE(1) 					       Primer3 User Manuals						   PRIMER3_CORE(1)

NAME
primer3_core - Designs primers for PCR SYNOPSIS
primer3_core [-format_output] [-strict_tags] [< input_file] DESCRIPTION
primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints. By default, primer3_core accepts input and produces output in Boulder-io format, a pre-XML text-based input/output format for program-to-program data interchange format. The Boulder-io format and the commands that primer3_core understands are described in the README file, which on Debian systems can be found in /usr/share/doc/primer3/. OPTIONS
-format_output Prints a more user-oriented report for each sequence. -strict_tags primer3_core echoes and ignores any tags it does not recognize, unless the -strict_tags flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer. Note The old flag -2x_compat is no longer supported. EXIT STATUS CODES
o 0 on normal operation. o -1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a .for, .rev or .int file (probably due to a protection problem). o -2 on out-of-memory. o -3 empty input. o -4 error in a "Global" input tag (message in PRIMER_ERROR). REFERENCE
Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386. SEE ALSO
ntdpal(1) oligotm(1) COPYRIGHT
Copyright (C) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of primer3_core. This manual page was written by Steffen Moeller <moeller@debian.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself. primer3_core 1.1.4 05/09/2008 PRIMER3_CORE(1)

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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)
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