A new approach for displaying identities and differences among aligned amino acid sequences

An algorithm is presented for computing degrees of sequence conservation found among aligned amino acid sequences. Sequence identities are calculated for each position of an alignment and average identity values of neighboring positions are figured. The average identity value of the whole alignment is chosen as a limit to discriminate between well and less conserved sequence sections. A second algorithm is given to calculate the degree of divergence of individual sequences compared to the other sequences of the alignment. The approach is easy to use on microcomputers and gives an exact picture of sequence identities and differences in order to determine, first, protein regions of high functional or structural importance among homologous proteins, and, second, significant differences of single sequences that may contribute to individual properties of the analysed protein. The method is illustrated by an example analysing a sequence alignment of higher plant nitrate reductases.