DNA sequence compression using the burrows-wheeler transform.
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.
Adjeroh
Don
D
Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506-6109, USA.
Zhang
Yong
Y
Mukherjee
Amar
A
Powell
Matt
M
Bell
Tim
T
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*
D004247:DNA