SA_overlapMatchesAlignment


Usage:

Score = SA_overlapMatchesAlignment(String1, String2, GapPenalty, ScoreTreshold)

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

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


Description

SA_overlapMatchesAlignment computes the overlap matches alignment score for the two strings String1 and String2 using GapPenalty for gaps and ScoreTreshold for individual scores. 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 parameters GapPenalty and ScoreTreshold are expected to be positive numbers as they will be substracted during the algorithm.




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