HSPp-BLAST: Highly Scalable Parallel PSI-BLAST for Very Large-scale Sequence Searches

摘要

Based on recent published articles, the growth of genomic data has overtaken and outpaced both performance improvements of storage technologies and processing power due to the revolutionary advancements of next generation sequencing technologies. By bringing down the costs and increasing throughput by many orders of magnitude with sequencing technologies, data is doubling every 9 months resulting in the exponential growth of genomic data in recent years. However, data analysis becomes increasingly difficult and can be prohibitive, as existing bioinformatics tools developed in the past decade focus mainly on desktops, workstations and small clusters that have limited capabilities. Improving the performance and scalability of such tools is critical to transforming ever-growing raw genomic data into biological knowledge containing invaluable information directly related to human health. This paper describes a new software application which includes optimization techniques improving the scalability of a most widely used bioinformatics tool "PSI-BLAST" on advanced parallel architectures, pushing the envelope of biological data analysis. We show that our improvements allow near-linear scaling to tens of thousands of processing cores, up to the maximum non-capability size on current petaflop supercomputers. This new tool increases by 5 orders of magnitude the amount of genomics data that can be processed per hour.