SA_repeatedMatchesAlignment
Usage:
Score = SA_repeatedMatchesAlignment(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_repeatedMatchesAlignment computes the repeated 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
-(K+10) = jump to position K of the String1 (Repeated Match)
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.
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