Abstract

Title: Distributed Searching in Biological Databases
Published: December 2005
Authors: Dominic Battré
Abstract: This thesis addresses the problem of searching huge biological databases on the scale of several gigabytes by utilizing parallel processing. Biological databases storing DNA sequences, protein sequences, or mass spectra are growing exponentially. Searches through these databases consume exponentially growing computational resources as well. The thesis demonstrates and analyzes a general use, MPI based, C++ framework for generically splitting databases amongst several computational nodes. The combined RAM of the nodes working in tandem is often sufficient to keep the entire database in memory, and therefore to search it efficiently without paging to disk. The framework runs as a persistent service, processing all submitted queries. This allows for query reordering and better utilization of the memory. Thereby, we achieve superlinear speedups compared to single processor implementations. We demonstrate the utility and speedup of the framework using a real biological database and an actual searching algorithm for Mass Spectrometry.
Full Paper: [pdf]