CONSTRUCTION AND EVALUATION OF AMINO ACID SUBSTITUTION MATRICES FOR OPTIMAL ALIGNMENT OFSEQUENCES OF MICROBIAL RHODOPSINS
Pairwise alignment of amino acid sequences is the basic tool of bioinformatics and it is widely used itself and in numerous approaches. Performance of this tool is critically depends on scoring function, which consisted of substitution matrix and gap penalties. In this work we constructed and evaluated a set of family-specific substitution matrices for microbial rhodopsins (RHOD) and compared them with general-purpose matrices (BLOSUM, VTML, PFASUM). We showed that all matrices demonstrated similar quality of pairwise alignment of microbial rhodopsins and only BLOSUM and VTML matrices, and linear combinations of them with RHOD matrices, are able to detect distant homology between microbial rhodopsins and heliorhodopsin.