Substitution Transformation of Score Matrix for Improving Alignment Quality of Local Sequence of Distantly Related Proteins

This paper presents a transformation method of original score matrix by correspondently normalizing its elements in row and column. The sequence alignment of 4830 superfamilies and 9570 fold related protein pairs showed that the quality of the alignment based on the transformed matrices is significantly improved compared to that based on the original matrices, especially for the fold related protein pairs, which is possibly due to that the elements in the transformed matrix contain more similarity information between two residues than those in the original matrix. These results indicate that for the sequence alignment of distantly related proteins, the original score matrix should probably be replaced by its correspondently transformed matrix to enhance the quality of sequence alignment.