HELIOS: High-speed sequence alignment in optics
Fig 5
Output explanation of the HELIOS method.
The output of the HELIOS method is represented with a two-row matrix, while the first and second rows are produced by the S1-align and S2-align operations, respectively. Moreover, each entry represents the alignment output of the characters at the corresponding position in the input sequences. By traversing the output from left to right, nonzero entries in both rows depict identical characters, i.e. character matching; while zero entries in both rows depict character mutation. Finally, a zero entry of a row along with a nonzero entry of the other one indicates indel, i.e. character insertion or deletion, and can be represented by a gap at the corresponding position of the sequence, containing the nonzero entry.