Entangled Effects of Two Consecutive Pairs in Residues and its Use in Alignment

In the previous paper, 1 we showed the significant improvement of sequence alignment can be done by considering the entanglement between two consecutive pairs of residues, in which we introduced a new measure defined on compound systems of two sequences which taking entanglement. In this paper, we explain the advantage of our new measure compared with the “sum of pairs” measure as the measure often-used, and we also show the performance evaluation of our algorithm against other six alignment methods. Our alignment is available at our webpage " http://www.rs.noda.tus.ac.jp/%7Eohya-m/".