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, Clustal Omega, 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. Author summary The character-by-character alignment of two long biological sequences, i.e. DNA, RNA, and protein, is a tedious task, but essential for recognizing homologies, relationships, and variations. In this case, every alteration, including mutations (substitution), and indels (insertion or deletion) is vital and required for many biological developments like diagnosis, medicine, and vaccination. However, the applicability of current sequence alignment methods is limited, specifically in processing time and memory usage, due to their inherent serialism and imperfections of electrical systems, as well as inefficient coding schemes of optical approaches. It approximately leads to quadratic run-time and space requirements in terms of input sequence lengths, becoming an expensive and laborious process for the real-time alignment of large datasets. Hence, proposing a superior alignment method in terms of accuracy, performance, and applicability can promote biological research and developments. Here, we show that we can overcome the long-lasting and challenging problems in sequence alignment procedure by exploiting optics as a novel computing technology. In this manner, we propose a novel method and its optical architecture for alignment of DNA, RNA, and protein sequences by exploiting high-speed processing and operational parallelism in optics. As our simulation studies confirm, it provides an accurate sequence alignment with outperforming the most widely used electrical and optical alternatives in the terms of processing time and memory requirements.

Automated summary

This paper presents a novel all-optical high-throughput method called HELIOS for aligning DNA, RNA, and protein sequences. The HELIOS method utilizes sophisticated operations to locate matches, mutations, and indels within biological sequences, while the optical architecture employs high-speed processing and operational parallelism. Simulation studies confirm that the HELIOS method outperforms both electrical and optical alternatives in terms of processing time and memory requirements.