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 © 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.