A Simple Statistical Algorithm for Biological Sequence Compression

Minh Duc Cao, Trevor I. Dix, Lloyd Allison, Chris Mears

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Abstract: This paper introduces a novel algorithm for biological sequence compression that makes use of both statistical properties and repetition within sequences. A panel of experts is maintained to estimate the probability distribution of the next symbol in the sequence to be encoded. Expert probabilities are combined to obtain the final distribution. The resulting information sequence provides insight for further study of the biological sequence. Each symbol is then encoded by arithmetic coding. Experiments show that our algorithm outperforms existing compressors on typical DNA and protein sequence datasets while maintaining a practical running time.
 
Minh Duc Cao, Trevor I. Dix, Lloyd Allison, Chris Mears.
A Simple Statistical Algorithm for Biological Sequence Compression.
IEEE Data Compression Conference (DCC), pp.43-52, 2007
[doi:10.1109/DCC.2007.7]['07]
[preprint.pdf]
 
Also see:
[BMC Bioinformatics '07], [Compression], [Bioinformatics],
and a related [seminar]
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© L. Allison   http://www.allisons.org/ll/   (or as otherwise indicated),
Faculty of Information Technology (Clayton), Monash University, Australia 3800 (6/'05 was School of Computer Science and Software Engineering, Fac. Info. Tech., Monash University,
was Department of Computer Science, Fac. Comp. & Info. Tech., '89 was Department of Computer Science, Fac. Sci., '68-'71 was Department of Information Science, Fac. Sci.)
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