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Scoring Matrices for Alignment

The SmithWaterman local alignment algorithm is used for the identification of the IGHV gene to simplify the HMM (1). JAligner, a java implementation of the algorithm is used by iHMMune-align. This is implemented with the Gotoh improvement (2). The SmithWaterman algorithm makes use of a scoring matrix to determine the 'best' alignment. The basis of the scoring is adding a set score for a match between two sequences and subtracting a penalty for a difference between the two seqeunces. The scoring matrix defines these match and mismatch scores.

A sample of the scoring matrix is shown below. The intercept of a row and column provide the score to be taken into account for an alignment between the corresponding nucleotides. Matrix files can be found from NCBI or the below can be cut and pasted into a text file and altered for use as a custom file with iHMMune-align. If a custom scoring matrix is used it is removed from the server as soon as the results are displayed.

#
# This matrix was created by Todd Lowe   12/10/92
#
# Uses ambiguous nucleotide codes, probabilities rounded to 
#  nearest integer
#
# Lowest score = -4, Highest score = 5
#
    A   T   G   C   S   W   R   Y   K   M   B   V   H   D   N
A   4  -5  -5  -5  -4   1   1  -4  -4   1  -4  -1  -1  -1  -2
T  -5   4  -5  -5  -4   1  -4   1   1  -4  -1  -4  -1  -1  -2
G  -5  -5   4  -5   1  -4   1  -4   1  -4  -1  -1  -4  -1  -2
C  -5  -5  -5   4   1  -4  -4   1  -4   1  -1  -1  -1  -4  -2
S  -4  -4   1   1  -1  -4  -2  -2  -2  -2  -1  -1  -3  -3  -1
W   1   1  -4  -4  -4  -1  -2  -2  -2  -2  -3  -3  -1  -1  -1
R   1  -4   1  -4  -2  -2  -1  -4  -2  -2  -3  -1  -3  -1  -1
Y  -4   1  -4   1  -2  -2  -4  -1  -2  -2  -1  -3  -1  -3  -1
K  -4   1   1  -4  -2  -2  -2  -2  -1  -4  -1  -3  -3  -1  -1
M   1  -4  -4   1  -2  -2  -2  -2  -4  -1  -3  -1  -1  -3  -1
B  -4  -1  -1  -1  -1  -3  -3  -1  -1  -3  -1  -2  -2  -2  -1
V  -1  -4  -1  -1  -1  -3  -1  -3  -3  -1  -2  -1  -2  -2  -1
H  -1  -1  -4  -1  -3  -1  -3  -1  -3  -1  -2  -2  -1  -2  -1  
D  -1  -1  -1  -4  -3  -1  -1  -3  -1  -3  -2  -2  -2  -1  -1
N  -2  -2  -2  -2  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1

References

1. T.F. Smith and Waterman, M.S., 1981, Identification of common molecular subsequences , Journal of Molecular Biology, 147:195-197, doi:10.1016/0022-2836(81)90087-5
2 O. Gotoh., 1982, An improved algorithm for matching biological sequences , Journal of Molecular Biology, 162:705-708, doi:10.1016/0022-2836(82)90398-9

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