HELIOS: High-speed sequence alignment in optics
Fig 8
Simulation outputs of the HELIOS method and its optical architecture.
In this case of study, the “Severe acute respiratory syndrome coronavirus 2” sequences [49] are aligned in the form of (A) Protein, (B) RNA, and (C) DNA; while some single and multiple mutations/indels are manually imposed to the sequence with varying distributions. For more clarity, only a small portion of each full-length alignment including 60 characters is shown in this figure, with the beginning at (A) character 240, (B) character 721, and (C) character 1921. In the coding and the alignment procedure, the parameters are set to R = 4 and k = 5. By investigating the outputs, two input sequences are successfully aligned in a two-line output by performing two consecutive procedures of the HELIOS method, as well as, passing optical beams through two units of the HELIOS optical architecture. As a result, the matches, mutations, and indels are detected and located accurately.