Optimizing I/O Cost and Managing Memory for Composition Vector Method Based on Correlation Matrix Calculation in Bioinformatics
Anaththa P.D. Krishnajith, Wayne Kelly and Yu-Chu Tian
Affiliation: School of Electrical Engineering and Computer Science, Queensland University of Tech, GPO Box 2434, Brisbane QLD 4001, Australia.
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.
Keywords: Bioinformatics computing, correlation matrix, memory management, phylogenetic analysis, scalable computing.
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