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Database Allocation Strategies for Parallel BLAST Evaluation on Clusters
Authors:Rogério Luís de Carvalho Costa  Sérgio Lifschitz
Institution:(1) Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rua Marquês de São Vicente 225, Rio de Janeiro, RJ 22453-900, Brasil
Abstract:In this work we investigate the parallel evaluation of BLAST, the most popular tool for comparing biological sequences. Our goal is to study database distribution issues that, besides workload balancing, could improve the performance of a set of BLAST processes running in a workstation cluster. We consider different partitioning strategies within actual BLAST executions against a few relevant molecular databases. We have implemented multiple databases and input sequence configurations and show that there are many important parameters, such as the fragment generation method and sequence similarities, that must be taken into account in order to make full use of such parallel environment.
Keywords:database design  data distribution  BLAST  parallelism  workstation clusters
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