Title: A Lossless Compression Algorithm for DNA sequences

Authors: Taysir H.A. Soliman, Tarek F. Gharib, Alshaimaa Abo-Alian, M.A. El Sharkawy

Addresses: Faculty of Computer and Information, Assiut University, Egypt. ' Faculty of Computer and Information Sciences, Ain Shams University, Egypt. ' Faculty of Computer and Information Sciences, Ain Shams University, Egypt. ' Faculty of Computer and Information Sciences, Ain Shams University, Egypt

Abstract: The increase of the amount of DNA sequences requires efficient computational algorithms for performing sequence comparison and analysis. Standard compression algorithms are not able to compress DNA sequences because they do not consider special characteristics of DNA sequences (i.e., DNA sequences contain several approximate repeats and complimentary palindromes). Recently, new algorithms have been proposed to compress DNA sequences, often using detection of long approximate repeats. The current work proposes a Lossless Compression Algorithm (LCA), providing a new encoding method. LCA achieves a better compression ratio than that of existing DNA-oriented compression algorithms, when compared to GenCompress, DNACompress, and DNAPack.

Keywords: LCA; lossless compression algorithm; encoding; approximate repeats; palindrome; DNA sequences; bioinformatics.

DOI: 10.1504/IJBRA.2009.029040

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.6, pp.593 - 602

Received: 16 Dec 2007
Accepted: 26 Aug 2008
Published online: 29 Oct 2009 *

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