129 lines
4.2 KiB
Groff
129 lines
4.2 KiB
Groff
'\" t
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.\" Title: NTDPAL
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.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
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.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
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.\" Date: 11/30/2011
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.\" Manual: Primer3 User Manuals
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.\" Source: ntdpal 1.1.4
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.\" Language: English
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.\"
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.TH "NTDPAL" "1" "11/30/2011" "ntdpal 1.1.4" "Primer3 User Manuals"
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.\" -----------------------------------------------------------------
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.\" * Define some portability stuff
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.\" -----------------------------------------------------------------
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.\" http://bugs.debian.org/507673
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.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.ie \n(.g .ds Aq \(aq
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.el .ds Aq '
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.\" -----------------------------------------------------------------
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.\" * set default formatting
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.\" -----------------------------------------------------------------
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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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.\" -----------------------------------------------------------------
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.\" * MAIN CONTENT STARTS HERE *
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.\" -----------------------------------------------------------------
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.SH "NAME"
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ntdpal \- Provides Primer3\*(Aqs alignment functionality
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.SH "SYNOPSIS"
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.HP \w'\fBntdpal\fR\ 'u
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\fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR}
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.SH "DESCRIPTION"
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.PP
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Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\*(Aqs alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&.
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.SH "OPTIONS"
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.PP
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\fB\-g\fR \fIgval\fR
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.RS 4
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\fIgval\fR
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is a (positive) float (\&.01 precision) specifying penalty for creating a gap respectively (the penalties are subtracted from the output score)
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.RE
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.PP
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\fB\-l\fR \fIval\fR
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.RS 4
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\fIlval\fR
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is a (positive) float (\&.01 precision) specifying penalty for lengthening a gap respectively (the penalties are subtracted from the output score)
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.RE
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.PP
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\fB\-a\fR
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.RS 4
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Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\&.
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.RE
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.PP
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\fB\-e\fR
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.RS 4
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Causes the end position of the alignment in both sequences to be printed\&. Do not confuse with the \*(Aqe\*(Aq
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\fImode\fR\&.
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.RE
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.PP
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\fB\-f1, \-f2, \-f3\fR
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.RS 4
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Force specific implementations\&. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\&.
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.RE
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.PP
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\fB\-h\fR
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.RS 4
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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\&.)
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.RE
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.PP
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\fB\-p\fR
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.RS 4
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Causes the alignment to be displayed on stderr\&.
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.RE
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.PP
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\fB\-s\fR
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.RS 4
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causes
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\fIonly\fR
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the score to printed\&.
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.RE
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.PP
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\fB\-m\fR \fImval\fR
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.RS 4
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is the maximum allowed gap (default is 3)\&.
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.RE
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.PP
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\fIseq1\fR and \fIseq2\fR
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.RS 4
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are the sequences to be aligned\&.
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.RE
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.PP
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\fImode\fR
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.RS 4
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is one of
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\fIg\fR,
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\fIG\fR,
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\fIl\fR, or
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\fIL\fR
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specifying a global, global end\-anchored, local, or local end\-anchored alignment respectively\&. For backward compatibility
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\fIe\fR
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is equivalent to
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\fIG\fR\&.
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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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\fBprimer3_core\fR(1)
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\fBoligotm\fR(1)
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.SH "COPYRIGHT"
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.br
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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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/usr/share/doc/primer3/copyright
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to read the licence of ntdpal\&.
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.PP
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This manual page was written by Charles Plessy <plessy@debian\&.org> 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 oligotm itself\&.
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.sp
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