HELIOS: High-speed sequence alignment in optics
Table 7
A brief report of the quantitative measurement of homology of measurement of the HELIOS method, compared to nine well-known algorithms, including SW, NW, BLAST, ClustalW, ClustalΩ, Muscle, T-Coffee, Kalign, and MAFFT. In this manner, the parameters Identity, Similarity, and Alignment Score are reported.
The Identity reports the number of exactly matched characters of two compared sequences (in percentage), aligned by each algorithm. Moreover, the Similarity measures the resemblance of two compared sequences (in percentage), aligned by every aformentioned algorithm. Various amino acids are categorized into six groups based on their physicochemical properties; including GAVLI, FYW, STCM, KRH, DENQ, and P. Finally, to calculate the Alignment Score of two compared sequences, aligned by every aforementioned algorithm, the BLOSUM62 substitution scoring matrix is adopted with gap opening and extension penalties equal to -10 and -0.5, respectively. Twelve diferent datasets are considered for this study [53, 55–61].