Optimizing I/O cost and managing memory for composition vector method based on correlation matrix calculation in bioinformatics

Krishnajith, Anaththa P.D., Kelly, Wayne A., & Tian, Yu-Chu (2014) Optimizing I/O cost and managing memory for composition vector method based on correlation matrix calculation in bioinformatics. Current Bioinformatics, 9(3), pp. 234-245.

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The generation of a correlation matrix for set of genomic sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. Each sequence may be millions of bases long and there may be thousands of such sequences which we wish to compare, so not all sequences may fit into main memory at the same time. Each sequence needs to be compared with every other sequence, so we will generally need to page some sequences in and out more than once. In order to minimize execution time we need to minimize this I/O. This paper develops an approach for faster and scalable computing of large-size correlation matrices through the maximal exploitation of available memory and reducing the number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different bioinformatics problems with different correlation matrix sizes. The significant performance improvement of the approach over previous work is demonstrated through benchmark examples.

Impact and interest:

3 citations in Scopus
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1 citations in Web of Science®

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ID Code: 74892
Item Type: Journal Article
Refereed: Yes
Keywords: Bioinformatics computing, Phylogenetic analysis, Memory management, Correlation matrix, Scalable computing
DOI: 10.2174/1574893609666140516005327
ISSN: 1574-8936
Divisions: Current > Schools > School of Electrical Engineering & Computer Science
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2014 Bentham Science Publishers Ltd.
Deposited On: 12 Aug 2014 01:56
Last Modified: 09 Aug 2015 18:50

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