Out of core computation of HSPs for large biological sequences

Abstract

Bioinformatics is facing a post-genomic era characterized by the release of large amounts of data boosted by the scientific revolution in high throughput technologies. This document presents an approach to deal with such a massive data processing problem in a paradigmatic application from which interesting lessons can be learned. The design of an out-of-core and modular implementation of traditional High-scoring Segment Pairs (HSPs) applications removes the limits of genome size and performs the work in linear time and with controlled computational requirements. Regardless of the expected huge I/O operations, the full system performs faster than state-of-the-art references providing additional advantages such as monitoring and interactive analysis, the exploitation of important intermediate results, and giving the specific nature of the modules, instead of monolithic software, enabling the plugging of external components to squeeze results. © 2013 Springer-Verlag Berlin Heidelberg.