A component-based implementation of multiple sequence alignment

Authors:
Umit Catalyurek;Mike Gray;Tahsin Kurc;Joel Saltz;Eric Stahlberg;Renato Ferreira
Affiliations:
The Ohio State University, Columbus, OH;The Ohio State University, Columbus, OH;The Ohio State University, Columbus, OH;The Ohio State University, Columbus, OH;Ohio Supercomputer Center, Columbus, OH;UFMG, Belo Horizonte, Brazil
Venue:
Proceedings of the 2003 ACM symposium on Applied computing
Year:
2003

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Abstract

This paper addresses the efficient execution of a Multiple Sequence Alignment (MSA) method, in particular the progressive alignment-based CLUSTAL W algorithm, on a cluster of workstations. We describe a scalable component-based implementation of CLUSTAL W program targeting distributed memory machines and multiple query workloads. We look at the effect of data caching on the performance of the data server. We present a distributed, persistent cache approach for caching intermediate results for reuse in subsequent or concurrent queries. Our initial results show that the cache-enabled CLUSTAL W program scales well on a cluster of workstations.