ntdpal1

Usage

Overview

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

mode

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.