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90 lines
3.2 KiB
Groff
90 lines
3.2 KiB
Groff
.\" Title: PRIMER3_CORE
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.\" Author:
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.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
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.\" Date: 05/09/2008
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.\" Manual: Primer3 User Manuals
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.\" Source: primer3_core 1.1.4
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.\"
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.TH "PRIMER3_CORE" "1" "05/09/2008" "primer3_core 1.1.4" "Primer3 User Manuals"
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.\" disable hyphenation
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.nh
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.\" disable justification (adjust text to left margin only)
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.ad l
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.SH "NAME"
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primer3_core \- Designs primers for PCR
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.SH "SYNOPSIS"
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.HP 13
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\fBprimer3_core\fR [\-format_output] [\-strict_tags] [<\ \fIinput_file\fR]
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.SH "DESCRIPTION"
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.PP
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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\&.
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.PP
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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
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\fIREADME\fR
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file, which on Debian systems can be found in
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\fI/usr/share/doc/primer3/\fR\&.
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.SH "OPTIONS"
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.PP
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\fB\-format_output\fR
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.RS 4
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Prints a more user\-oriented report for each sequence\&.
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.RE
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.PP
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\fB\-strict_tags\fR
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.RS 4
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primer3_core echoes and ignores any tags it does not recognize, unless the
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\fB\-strict_tags\fR
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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\&.
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.RE
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.sp
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.it 1 an-trap
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.nr an-no-space-flag 1
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.nr an-break-flag 1
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.br
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Note
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.PP
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The old flag \-2x_compat is no longer supported\&.
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.SH "EXIT STATUS CODES"
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.sp
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.RS 4
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\h'-04'\(bu\h'+03'0 on normal operation\&.
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.RE
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.sp
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.RS 4
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\h'-04'\(bu\h'+03'\-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)\&.
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.RE
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.sp
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.RS 4
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\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\&.
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.RE
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.sp
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.RS 4
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\h'-04'\(bu\h'+03'\-3 empty input\&.
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.RE
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.sp
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.RS 4
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\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\&.
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.RE
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.SH "REFERENCE"
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.PP
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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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.SH "SEE ALSO"
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.PP
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\fBntdpal\fR(1)
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\fBoligotm\fR(1)
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.SH "COPYRIGHT"
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Copyright \(co 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
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.br
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.PP
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All rights reserved\&. On Debian\-based systems, please consult
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\fI/usr/share/doc/primer3/copyright\fR
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to read the licence of primer3_core\&.
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.PP
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This manual page was written by Steffen Moeller
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<moeller@debian\&.org>
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for the
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Debian(TM)
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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\&.
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.sp
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