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
· 0 on normal operation.
· -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).
· -2 on out-of-memory.
· -3 empty input.
· -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 © 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.