SA_localAlignment


Usage:

Score = SA_localAlignment(String1, String2, GapPenalty)

String1: [M x k] Matrix; The first string.
String2: [N x k] Matrix; The second string.
GapPenalty: Float; The gap penalty parameter.

Score: [T+1 x 1] Matrix; The score of the alignment and the alignment itself.


Description

SA_localAlignment computes the Smith-Waterman alignment score for the two strings String1 and String2 using GapPenalty for gaps. The input strings are expected to be of the form [L x k] where L can be variable for each string and k must be the same, as it is the vector dimension.
The result Score is a [T+1 x 1] Vector with the first element beeing the score. The remaining T elements are the alignment in form of numbers:
1 = Match
2 = Gap in String1
3 = Gap in String2
-1 = ignore element in String1
-2 = ignore element in String2


The score between two vectors of the string is computed by the correlation between those two.

NOTE: The parameter GapPenalty is expected to be a positive number as it will be substracted during the algorithm.




Copyright © 2007 Thomas Oskam, ETH Zürich. All rights reserved.