HELIOS: High-speed sequence alignment in optics.

In response to the imperfections of current sequence alignment methods, originated from the inherent serialism within their corresponding electrical systems, a few optical approaches for biological data comparison have been proposed recently. However, due to their low performance, raised from their inefficient coding scheme, this paper presents a novel all-optical high-throughput method for aligning DNA, RNA, and protein sequences, named HELIOS. The HELIOS method employs highly sophisticated operations to locate character matches, single or multiple mutations, and single or multiple indels within various biological sequences. On the other hand, the HELIOS optical architecture exploits high-speed processing and operational parallelism in optics, by adopting wavelength and polarization of optical beams. For evaluation, the functionality and accuracy of the HELIOS method are approved through behavioral and optical simulation studies, while its complexity and performance are estimated through analytical computation. The accuracy evaluations indicate that the HELIOS method achieves a precise pairwise alignment of two sequences, highly similar to those of Smith-Waterman, Needleman-Wunsch, BLAST, MUSCLE, ClustalW, ClustalΩ, T-Coffee, Kalign, and MAFFT. According to our performance evaluations, the HELIOS optical architecture outperforms all alternative electrical and optical algorithms in terms of processing time and memory requirement, relying on its highly sophisticated method and optical architecture. Moreover, the employed compact coding scheme highly escalates the number of input characters, and hence, it offers reduced time and space complexities, compared to the electrical and optical alternatives. It makes the HELIOS method and optical architecture highly applicable for biomedical applications.