A component-based implementation of multiple sequence alignment

Umit Catalyurek; Mike Gray; Tahsin Kurc; Joel Saltzt; Eric Stahlberg; Renato Ferreira

doi:10.1145/952532.952559

A component-based implementation of multiple sequence alignment

Umit Catalyurek
, Mike Gray
, Tahsin Kurc
, Joel Saltzt
, Eric Stahlberg
, Renato Ferreira

Biomedical Informatics

Ohio State University
Ohio Supercomputer Center
Universidade Federal de Minas Gerais

Research output: Contribution to conference › Paper › peer-review

12 Scopus citations

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.

Original language	English
Pages	122-126
Number of pages	5
DOIs	https://doi.org/10.1145/952532.952559
State	Published - 2003
Event	Proceedings of the 2003 ACM Symposium on Applied Computing - Melbourne, FL, United States Duration: Mar 9 2003 → Mar 12 2003

Conference

Conference	Proceedings of the 2003 ACM Symposium on Applied Computing
Country/Territory	United States
City	Melbourne, FL
Period	03/9/03 → 03/12/03

Keywords

Component-based architecture
Distributed computing
Multiple sequence alignment
Persistent data caching

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10.1145/952532.952559

Cite this

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title = "A component-based implementation of multiple sequence alignment",

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.",

keywords = "Component-based architecture, Distributed computing, Multiple sequence alignment, Persistent data caching",

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year = "2003",

doi = "10.1145/952532.952559",

language = "English",

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T1 - A component-based implementation of multiple sequence alignment

AU - Catalyurek, Umit

AU - Gray, Mike

AU - Kurc, Tahsin

AU - Saltzt, Joel

AU - Stahlberg, Eric

AU - Ferreira, Renato

PY - 2003

Y1 - 2003

N2 - 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.

AB - 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.

KW - Component-based architecture

KW - Distributed computing

KW - Multiple sequence alignment

KW - Persistent data caching

UR - https://www.scopus.com/pages/publications/0037661304

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DO - 10.1145/952532.952559

M3 - Paper

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EP - 126

T2 - Proceedings of the 2003 ACM Symposium on Applied Computing

Y2 - 9 March 2003 through 12 March 2003

ER -

A component-based implementation of multiple sequence alignment

Abstract

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Keywords

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