Research On A Profile Based Alignment Method For Protein Sequences

With the development of bioinformatics, a large number of proteins need for analysis. However for many protein sequences, the human is not clear evolutionary relationships between them, or the biological function. Protein sequence alignment is useful for determining evolutionary relationships of protein, and forecasting the biological function.This paper introduces some protein sequence alignment methods which are widely used, and their characteristics are summarized. Then profile method is described. At last, profile method and BLAST method are compared.In profile method two profiles are calculated respectively in accordance with related sequences of the two query sequences at first; and then a relationship matrix is calculated by comparing the two profiles; the alignment is calculated by dynamic programming with the relationship matrix. Finally, the relationship of the two query sequences is evaluated according to the alignment. Experimental data show that profile method provides higher accuracy than BLAST method, when the length of test protein sequences is long.