Optimizing amino acid substitution matrices with a local alignment kernel |
| |
Authors: | Hiroto Saigo Jean-Philippe Vert Tatsuya Akutsu |
| |
Affiliation: | (1) Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan;(2) Center for Computational Biology, Ecole des Mines de Paris, 35 rue Saint-Honor, 77300 Fontainebleau, France |
| |
Abstract: | Background Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, called a local alignment kernel, that exhibits good performance for this task in combination with a support vector machine. The local alignment kernel depends on an amino acid substitution matrix. Since commonly used BLOSUM or PAM matrices for scoring amino acid matches have been optimized to be used in combination with the Smith-Waterman algorithm, the matrices optimal for the local alignment kernel can be different. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|