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Matos-2013b

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Article

Title A compression model for DNA multiple sequence alignment blocks
Author Luís Matos, Diogo Pratas, Armando J. Pinho
Journal IEEE Transactions on Information Theory
Volume 59
Number 5
Pages 3189-3198
Month May
Year 2013
DOI 10.1109/TIT.2012.2236605
Group
Group (before 2015) Signal Processing Laboratory, Transverse Activity on Innovative Biomedical Technologies
Indexed by ISI Yes

Abstract - A particularly voluminous data set in molecular genomics, known as whole genome alignments, has gained considerable importance over the last years. In this paper, we propose a compression modeling approach for the multiple sequence alignment (MSA) blocks, that make up most of these data sets. Our method is based on a mixture of finite-context models. Contrarily to other recent approaches, it addresses both the DNA bases and gap symbols at once, better exploring the existing correlations. For comparison with previous methods, our algorithm was tested in the multiz28way data set. On average, it attained 0.94 bits per symbol, approximately 7% better than the previous best, for a similar computational complexity. We also tested the model in the most recent data set, multiz46way. In this data set, that contains aligments of 46 different species, our compression model achieved an average of 0.72 bits per MSA block symbol.

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