Abstract
Rapid advancements in research in the field of DNA sequence discovery has led to a vast range of compression algorithms. The number of bits required for storing four bases of any DNA sequence is two, but efficient algorithms have pushed this limit lower. With the constant decrease in prices of memory and communication channel bandwidth, one often doubts the need of such compression algorithms. The algorithm discussed in this chapter compresses the DNA sequence, and also allows one to generate finite length sequences, which can be used to find approximate pattern matches. DNA sequences are mainly of two types, Repetitive and Non-Repetitive. The compression technique used is meant for the non-repetitive parts of the sequence, where we make use of the fact that a DNA sequence consists of only 4 characters. The algorithm achieves bit/base ratio of 1.3-1.4(dependent on the database), but more importantly one of the stages of the algorithm can be used for efficient discovery of approximate patterns.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Rivals, E., Delahaye, J.-P., Dauchet, M., Delgrange.: A Guaranteed Compression Scheme for Repetitive DNA Sequences. LIFL Lille I University Technical Report (1995)
Matsumuto, T., Sadakane, K., Imai, H.: Biological Sequences Compression Algorithms. Genome Information Ser. Workshop Genome Inform 11, 43–52 (2000)
Grumbach, S., Tahi, F.: Compression of DNA Sequences. In: Data Compression Conference, pp. 340–350 (1993)
Grumbach, S., Tahi, F.: A New Challenge for Compression Algorithms Genetic Sequences. Journal of Information Processing and Management 30, 866–875 (1994)
Ziv, J., Limpel, A.: Compression of Individual Sequences using Variable-Rate Encoding. IEE Transactions on Information Theory 24, 530–536 (1978)
Ziv, J., Limpel, A.: A Universal Algorithm for Sequential Data Compression. IEE Transactions on Information Theory 23(3), 337–343 (1977)
Sadel, I.: Universal Data Compression Algorithm based on Approximate String Matching. In: Probability in the Engineering and Informational Sciences, pp. 465–486 (1996)
Chen, X., Kwong, S., Li, M.: A Compression Algorithm for DNA Sequences and its Application in Genome Comparison. Genomic 12, 512–514 (2001)
Chen, X., Kwong, S., Li, M.: A Compression Algorithm for DNA Sequences. IEEE Engineering in Medicine and Biology Magazine 20(4), 61–66 (2001)
Li, M., Badger, J.H., Chen, J.H., Kwong, S., Kerney, P., Zhang, H.: An Information based Sequences Distance and its Application to whole Mitochondrial Genome. Bioinformatics 17(2), 149–154 (2001)
Chen, X., La, M., Ma, B., Tromp, J.: DnaCompress: Fast and Selective DNA Sequence Compression. Bioinformatics 18, 1696–1698 (2002)
Ma, B., Tromp, J., Li, M.: Patternhunter-faster and more sensitive homology search. Bioinformatics 18, 440–445 (2002)
Sata, H., Yoshioka, T., Konagaya, A., Toyoda, T.: DNA Compression in the Post Genomic Era. Genome Informatics 12, 512–514 (2001)
Willems, F.M.J., Shtralov, Y.M., Tjalkens, T.J.: The Context Tree Weighting Method: Basic Properties. IEE Transactions on Information Theory 41(3), 653–664 (1995)
Sadakane, K., Okazaki, T., Imai, H.: Implementing the Context Tree Weighting Method for Text Compression. In: DCC 2000: Proceedings of the Conference on Data Compression, USA (2000)
Rivals, E., Dauchet, M.: Fast Discerning Repeats in DNA Sequences with a Compression Algorithm. In: Proceedings of Genome Informatics Workshop, pp. 215–226. Universal Academy Press, Tokyo (1997)
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Venugopal, K.R., Srinivasa, K.G., Patnaik, L.M. (2009). Probabilistic Approach for DNA Compression. In: Soft Computing for Data Mining Applications. Studies in Computational Intelligence, vol 190. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00193-2_14
Download citation
DOI: https://doi.org/10.1007/978-3-642-00193-2_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00192-5
Online ISBN: 978-3-642-00193-2
eBook Packages: EngineeringEngineering (R0)