title: DNA sequence compression using the burrows-wheeler transform.
abstract: We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns is an important phenomenon in biological sequences. Here, we propose off-line methods to compress DNA sequences that exploit the different repetition structures inherent in such sequences. Repetition analysis is performed based on the relationship between the BWT and important pattern matching data structures, such as the suffix tree and suffix array. We discuss how the proposed approach can be incorporated in the BWT compression pipeline.
authors.affiliation: Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506-6109, USA.
authors.forename: Don
authors.initials: D
authors.lastname: Adjeroh
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Amar
authors.initials: A
authors.lastname: Mukherjee
authors.forename: Matt
authors.initials: M
authors.lastname: Powell
authors.forename: Tim
authors.initials: T
authors.lastname: Bell
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000145:classification*; D044962:Data Compression / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA