primer3_core - Online in the Cloud

PROGRAM:

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.

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