table of contents
PRIMER3_CORE(1) | Primer3 User Manuals | PRIMER3_CORE(1) |
NAME¶
primer3_core - Designs primers for PCRSYNOPSIS¶
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_outputPrints 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.
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 Skaletsky05/09/2008 | primer3_core 1.1.4 |