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Breakthrough in applying optical processing for DNA sequence alignment

13th February 2018


Optalysys, a start-up commercialising light-speed optical coprocessors for AI/deep learning, and world-leading genomic research institute the Earlham Institute, EI, have announced the successful completion of the Genetic Search System (GENESYS) project. The GENESYS project, which was granted £0.5m in funding from Innovate UK, applied Optalysys' optical processing technology to perform large-scale DNA sequence alignment. 

The collaboration set out to provide a scalable, energy-efficient solution to this challenging high-performance computing (HPC) task. The benchmark case study for the project aligned metagenomic reads sequenced from the Human Microbiome Project Mock Community (a well characterised microbial community) against a database consisting of 20 bacterial genomes totalling 64 million base pairs. The optical system exceeded the original targets delivering a 90% energy efficiency saving compared to the same test run on EI's HPC cluster, with an accuracy comparable to the highly sensitive nucleotide form of BLAST, BLASTn (part of a family of Basic Local Alignment Search Tools used to compare query sequences with a library or database of sequences).

The project results also revealed the technology holds significant promise for long-read sequence alignment, where speed improvements of several orders of magnitude over conventional software algorithms are possible ­ as well as in Deep Learning, specifically convolutional neural networks (CNNs).  

The technology resulting from this project is launching in February 2018 as a cloud-based platform to a closed beta program of a select group of genomic institutes including EI (UK), The University of Manchester (UK), Oregon State University (USA), and Zealquest Scientific Technology in cooperation with the Shanghai Bioinformatics Center, Chinese Academy of Science.

"The collaboration with EI has been a great success," said Dr. Nick New, founder and CEO of Optalysys. "We have demonstrated the technology at several international conferences including Advances in Genome Biology and Technology, Plant and Animal Genome Conference and Genome 10K/Genome Science, to an overwhelmingly enthusiastic response. We are looking forward to continuing our strong relationship with EI through the beta program and beyond."

"Genomic institutes are being faced with analysing more and more data, and it is really exciting that new technologies like the Optalysys optical processing platform can support bioinformaticians processing data accurately, at a low cost and at high speeds," said Dr Daniel Mapleson, Analysis Pipelines Project Leader at EI who was the EI lead for the genomics tests during the project. 

Jon Mitchener, innovation lead for emerging technologies, Innovate UK, said, "GENESYS is a project that not only exemplifies the R&D done (combining novel optical HPC and deep learning AI techniques with a really important health-screening application), but also the way that support from Innovate UK can help accelerate the move from a prototype towards commercial product launch for a high-potential British SME like Optalysys."






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