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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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NTDPAL(1)						       Primer3 User Manuals							 NTDPAL(1)

NAME
ntdpal - Provides Primer3's alignment functionality SYNOPSIS
ntdpal [-g gval] [-l lval] [-m mval] [-f1, f2, f3] [-p] [-s] [-e] {seq1} {seq2} {mode} DESCRIPTION
Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand-alone program that provides Primer3's alignment functionality (local, a.k.a. Smith-Waterman, global, a.k.a. Needleman-Wunsch, plus "half global"). OPTIONS
-g gval gval is a (positive) float (.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score) -l val lval is a (positive) float (.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score) -a Causes the scoring matrix to be modified by dpal_set_ambiguity_codes. -e Causes the end postion of the alignment in both sequences to be printed. Do not confuse with the 'e' mode. -f1, -f2, -f3 Force specific implementations. -f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed. -h Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = -0.5. (The default scoring matrix assigns 1 to a match, and -1 to a mismatch.) -p Causes the alignment to be displayed on stderr. -s causes only the score to printed. -m mval is the maximum allowed gap (default is 3). seq1 and seq2 are the sequences to be aligned. mode is one of g, G, l, or L specifying a global, global end-anchored, local, or local end-achored alignment respectively. For backward compatibility e is equivalent to G. 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) 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 ntdpal. 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. ntdpal 1.1.4 05/09/2008 NTDPAL(1)
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