data compression concepts and algorithms and their applications to bioinformatics数据压缩的概念和算法及其应用生物信息学.pdf

Entropy 2010, 12, 34-52; doi:10.3390/ OPEN ACCESS entropy ISSN 1099-4300 /journal/entropy Review Data Compression Concepts and Algorithms and Their Applications to Bioinformatics ¨ ˜ Ozkan U. Nalbantoglu, David J. Russell and Khalid Sayood Department of Electrical Engineering, University of Nebraska-Lincoln, NE 68588-0511, USA; E-Mails: nalbantoglu@ (O.U.N.); drussell@ (D.J.R.) Author to whom correspondence should be addressed; E-Mail: ksayood@; Tel.: +1-402-472-6688; Fax: +1-402-472-4732. Received: 04 December 2009 / Accepted: 17 December 2009 / Published: 29 December 2009 Abstract: Data compression at its base is concerned with how information is organized in data. Understanding this organization can lead to efficient ways of representing the information and hence data compression. In this paper we review the ways in which ideas and approaches fundamental to the theory and practice of data compression have been used in the area of bioinformatics. We look at how basic theoretical ideas from data compression, such as the notions of entropy, mutual information, and complexity have been used for analyzing biological sequences in order to discover hidden patterns, infer phylogenetic relationships between organisms and study viral populations. Finally, we look at how inferred grammars for biological sequences have been used to uncover structure in biological sequences. Keywords: bioinformatics; data co