ntdpal - Online in the Cloud

PROGRAM:

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 penalty for creating a gap
respectively (the penalties are subtracted from the output score)

-l val
lval is a (positive) float (.01 precision) specifying penalty 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 position 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-anchored 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.

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