Handling biological sequence alignments on networked computing systems: A divide-and-conquer approach

In this paper, we address the biological sequence alignment problem, which is one of the most commonly used steps in several bioinformatics applications. We employ the Divisible Load Theory (DLT) paradigm that is suitable for handling large-scale processing on network-based systems to achieve a high...

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Bibliographic Details
Published in:	Journal of parallel and distributed computing Vol. 69; no. 10; pp. 854 - 865
Main Authors:	Bharadwaj, Veeravalli, Wong, Han Min
Format:	Journal Article
Language:	English
Published:	Amsterdam Elsevier Inc 01.10.2009 Elsevier
Subjects:	Analytical, structural and metabolic biochemistry Applied sciences Biological and medical sciences Biological sequences Communication delay Computer science; control theory; systems Data processing. List processing. Character string processing Divisible load theory Exact sciences and technology Fundamental and applied biological sciences. Psychology Gene expression General aspects General aspects, investigation methods Linear networks Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Memory organisation. Data processing Molecular and cellular biology Molecular genetics Proteins Sequence alignment Smith–Waterman algorithm Software Communication delay Smith–Waterman algorithm Linear networks Biological sequences Sequence alignment Divisible load theory Data analysis Computer simulation Transmission protocol Interconnected power system DNA sequence Processing time Smith-Waterman algorithm Distributed computing Transmission time Workload Minimum time DNA Optimal solution Heuristic method Database Parallelism Bioinformatics Divide and conquer method
ISSN:	0743-7315, 1096-0848
Online Access:	Get full text
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