Improving performance of multiple sequence alignment analysis in multi-client environments
Ümit V. Çatalyürek,Eric Stahlberg,Renato Ferreira,Tahsin Kurc,J. Saltz +4 more
- 15 Apr 2002
- pp 183
TL;DR: An approach for caching intermediate results for reuse in subsequent or concurrent queries, in particular the CLUSTAL W algorithm, which focuses on progressive alignment-based strategies and shows that the cache-enabled CLUSTal W program scales well on a SMP machine.
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Abstract: This paper is concerned with the efficient execution of multiple sequence alignment methods in a multiple client environment. Multiple sequence alignment (MSA) is a computationally expensive method, which is commonly used in computational and molecular biology. Large databases of protein and gene sequences are available to the scientific community. Oftentimes, these databases are accessed by multiple users to execute MSA queries. The data server has to handle multiple concurrent queries in such situations. We look at the effect of data caching on the performance of the data server. We describe an approach for caching intermediate results for reuse in subsequent or concurrent queries. We focus on progressive alignment-based strategies, in particular the CLUSTAL W algorithm. Our results for 350 sets of sequences show an average speedup of up to 2.5 is obtained by caching intermediate results. Our results also show that the cache-enabled CLUSTAL W program scales well on a SMP machine.
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Citations
BioBench: A Benchmark Suite of Bioinformatics Applications
K. Albayraktaroglu,Aamer Jaleel,X. Wu,M. Franklin,Bruce Jacob,Chau-Wen Tseng,Donald Yeung +6 more
- 20 Mar 2005
TL;DR: The evaluation suggests that bioinformatics applications have distinctly different characteristics from the applications in both of the mentioned SPEC suites; and the findings indicate that bioInformatics workloads can benefit from architectural improvements to memory bandwidth and techniques that exploit their high levels of ILP.
MT-ClustalW: multithreading multiple sequence alignment
Kridsadakorn Chaichoompu,Surin Kittitornkun,Sissades Tongsima +2 more
- 25 Apr 2006
TL;DR: The experiment results show that the MT-ClustalW framework can achieve a considerable speedup over the sequential ClUSTalW and original multithreaded Clustal W-SMP implementations.
Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine
Adrianto Wirawan,Bertil Schmidt,Chee Keong Kwoh +2 more
- 20 May 2009
TL;DR: It is demonstrated how the PlayStation®3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the distance matrix computation utilized in multiple sequence alignment algorithms.
A component-based implementation of multiple sequence alignment
Ümit V. Çatalyürek,Michael R. Gray,Tahsin Kurc,Joel H. Saltz,Eric Stahlberg,Renato Ferreira +5 more
- 09 Mar 2003
TL;DR: 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, and presents a distributed, persistent cache approach for caching intermediate results for reuse in subsequent or concurrent queries.
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References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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