Distributed BLAST in a grid computing context

Bayer, M. and Sinnott, R.O. (2005) Distributed BLAST in a grid computing context. Lecture Notes in Computer Science, 3695, pp. 241-252. (doi: 10.1007/11560500_22)

Abstract

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems.

• Item Type: Articles
• Additional Information: The original publication is available at www.springerlink.com
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Sinnott, Professor Richard
• Authors: Bayer, M., and Sinnott, R.O.
• Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
• College/School: University Services > IT Services > Computing Service
• Journal Name: Lecture Notes in Computer Science
• Publisher: Springer
• ISSN: 0302-9743
• ISSN (Online): 1611-3349
• Published Online: 28 September 2005
• Copyright Holders: Copyright © 2005 Springer
• First Published: First published in Lecture Notes in Computer Science 3695:241-252
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher.