HELIOS: High-speed sequence alignment in optics
Fig 4
Side-by-side representation of the S1-align and S2-align operations of the HELIOS method.
(A) As an overall view, the S1-align operation locates character substitutions, as well as character insertions in S1 (or character deletions from S2). For this purpose, it compares the main and all shifted S2 vectors with the S1 vector. Afterward, to produce the 1D output vector, the ith entry of the output is determined according to the ith and (i + k)th entries of the comparison outcome vector. (B) Similarly, the S2-align operation compares the main and all shifted S1 vectors with the S2 vector to locate character substitutions, as well as character insertions in S2 (i.e. character deletions from S1).