HELIOS: High-speed sequence alignment in optics
Table 6
The parameter Alignment Score of the Smith-Waterman algorithm in the quantitative measurement of homology.
To calculate the Alignment Score of two compared sequences aligned by the HELIOS method, the BLOSUM62 substitution scoring matrix is adopted with gap opening and extension penalties equal to -10 and -0.5, respectively. Moreover, the “Nine ND5 protein sequences dataset” [53] is assumed in this study.