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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)

Check Out this Related Man Page

E-PCR(1)						      General Commands Manual							  E-PCR(1)

NAME

       e-PCR -- Find sequence tagged sites (STS) in DNA sequences

SYNOPSIS

       e-PCR [-hV] [posix-options] stsfile [fasta ...] [compat-options]

DESCRIPTION

       The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product.

OPTIONS

       posix-options are:

       -m=##	 Margin (default 50)

       -w=##	 Wordsize  (default 7)

       -n=##	 Max mismatches allowed (default 0)

       -g=##	 Max indels allowed (default 0)

       -f=##	 Use ## disontiguous words, slow if ##>1

       -o=##	 Set output file

       -t=##	 Set output format:

		 1 - classic, range (pos1..pos2)

		 2 - classic, midpoint

		 3 - tabular

		 4 - tabular with alignment in comments (slow)

       -d=##-##  Set default size range (default 100-350)

       -p=+-	 Turn hits postprocess on/off

       -v=##	 Verbosity flags

       -a=a|f	 Use presize alignments (only if gaps>0), slow

		 a - Always or f - as Fallback

       -x=+-	 Use 5'-end lowercase masking of primers (default -)

       -u=+-	 Uppercase all primers (default -)

       compat-options (duplicate posix-options) are

       M=##	 Margin (default 50)

       W=##	 Wordsize  (default 7)

       N=##	 Number of mismatches allowed (default 0)

       G=##	 Max indels allowed (default 0)

       F=##	 Use ## discontinuous words

       O=##	 Set output file to ##

       T=##	 Set output format (1..3)

       D=##-##	 Set default size range

       P=+-	 Postprocess hits on/off

       V=##	 Verbosity flags

       A=a|f	 Use presize alignments (only if gaps>0), slow

		 a - Always or f - as Fallback

       X=+-	 Use 5'-end lowercase masking of primers (default -)

       U=+-	 Uppercase all primers (default -)

       -mid	 Same as T=2

       For information about further options just call e-PCR without any options.

SEE ALSO

       /usr/share/doc/ncbi-epcr/README.txt

       bioperl(1), re-pcr(1)

AUTHORS

       This manual page was written by Steffen Moeller <moeller@debian.org> and Andreas Tille <tille@debian.org> for the Debian system (but may be
       used by others).  Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public  License,
       Version 2 any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   February 2004							  E-PCR(1)
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