Detailed assessment of homology detection using different substitution matrices  

作　　者：LI Jing WANG Wei 

机构地区：[1]National Lab of Solid State Microstructure, Department of Physics, and Institute of Biophysics, Nanjing University, Nanjing 210093, China

出　　处：《Chinese Science Bulletin》2006年第13期1538-1545,共8页

基　　金：supported by the National Natural Science Foundation of China(Grant Nos.90403120,10474041,and 10021001);the Nonlinear Project(973)of the NSM.

摘　　要：Homology detection plays a key role in bioinformatics, whereas substitution matrix is one of the most important components in homology detec- tion. Thus, besides the improvement of alignment algorithms, another effective way to enhance the accuracy of homology detection is to use proper substitution matrices or even construct new matrices. A study on the features of various matrices and on the comparison of the performances between differ- ent matrices in homology detection enable us to choose the most proper or optimal matrix for some specific applications. In this paper, by taking BLOSUM matrices as an example, some detailed features of matrices in homology detection are stud- ied by calculating the distributions of numbers of recognized proteins over different sequence identities and sequence lengths. Our results clearly showed that different matrices have different preferences and abilities to the recognition of remote homologous proteins. Furthermore, detailed features of the vari- ous matrices can be used to improve the accuracy of homology detection.Homology detection plays a key role in bioinformatics, whereas substitution matrix is one of the most important components in homology detection. Thus, besides the improvement of alignment algorithms, another effective way to enhance the accuracy of homology detection is to use proper substitution matrices or even construct new matrices. A study on the features of various matrices and on the comparison of the performances between different matrices in homology detection enable us to choose the most proper or optimal matrix for some specific applications. In this paper, by taking BLOSUM matrices as an example, some detailed features of matrices in homology detection are studied by calculating the distributions of numbers of recognized proteins over different sequence identities and sequence lengths. Our results clearly showed that different matrices have different preferences and abilities to the recognition of remote homologous proteins. Furthermore, detailed features of the various matrices can be used to improve the accuracy of homology detection.

关 键 词：替代矩阵 序列一致性 序列长度 同种探测 

分 类 号：Q811.4[生物学—生物工程]