Distributed BLAST in a Grid Computing Context

• Published in: Computational Life Sciences pp. 241 - 252
• Main Authors: Bayer, Micha M., Sinnott, Richard
• Format: Book Chapter Conference Proceeding
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2005; Springer
• Edition: 1ère éd
• Series: Lecture Notes in Computer Science
• Subjects: Applied sciences; Basic Local Alignment Search Tool; Basic Local Alignment Search Tool Search; Biological and medical sciences; Bridge Project; Computer science; control theory; systems; Computer systems and distributed systems. User interface; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General aspects; Globus Toolkit; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Software; Target Database; Bioinformatics; Sequence alignment
• ISBN: 3540291040; 9783540291046
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/11560500_22

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.