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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)

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OLIGOTM(1)						       Primer3 User Manuals							OLIGOTM(1)

NAME
oligotm - Prints oligo's melting temperature on stdout SYNOPSIS
oligotm [OPTIONS] {oligo} where oligo is a DNA sequence of between 2 and 36 bases DESCRIPTION
oligotm prints the melting temperature of a given desoxyribooligonucleotide on the standard output. It is part of the oligotm library. OPTIONS
-mv monovalent_conc Concentration of monovalent cations in mM, by default 50 mM. -dv divalent_conc Concentration of divalent cations in mM, by default 0 mM. -n dNTP_conc Concentration of deoxynycleotide triphosphate in mM, by default 0 mM. -d dna_conc Concentration of DNA strands in nM, by default 50 nM. -tp [0|1] Specifies the table of thermodynamic parameters and the method of melting temperature calculation: o 0 Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but not the recommended value. o 1 Use nearest neighbor parameter from SantaLucia 1998. This is the recommended value. -sc [0..2] Specifies salt correction formula for the melting temperature calculation: o 0 Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but not the recommended value. o 1 SantaLucia 1998. This is the recommended value. o 1 Owczarzy et al., 2004. -i prints references to publications which were used for thermodynamic calculations. 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
primer3_core(1) ntdpal(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 oligotm. This manual page was written by Charles Plessy <plessy@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 oligotm itself. oligotm 1.1.4 05/09/2008 OLIGOTM(1)
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