An Adaptive Difference Distribution-based Coding with Hierarchical Tree Structure for DNA Sequence Compression.
Previous reference-based compression on DNA sequences do not fully exploit the intrinsic statistics by merely concerning the approximate matches. In this paper, an adaptive difference distribution-based coding framework is proposed by the fragments of nucleotides with a hierarchical tree structure. To keep the distribution of difference sequence from the reference and target sequences concentrated, the sub-fragment size and matching offset for predicting are flexible to the stepped size structure. The matching with approximate repeats in reference will be imposed with the Hamming-like weighted distance measure function in a local region closed to the current fragment, such that the accuracy of matching and the overhead of describing matching offset can be balanced. A well-designed coding scheme will make compact both the difference sequence and the additional parameters, e.g. sub-fragment size and matching offset. Experimental results show that the proposed scheme achieves 150% compression improvement in comparison with the best reference-based compressor GReEn.
Department of Electronic Engineering Shanghai Jiaotong University Shanghai 200240, China, daiwenrui@sjtu.edu.cn.
Wenrui
W
Dai
Department of Electronic Engineering Shanghai Jiaotong University Shanghai 200240, China, xionghongkai@sjtu.edu.cn.
Hongkai
H
Xiong
Division of Biomedical Informatics University of California, San Diego San Diego, CA 92093, USA, x1jiang@ucsd.edu.
Xiaoqian
X
Jiang
Division of Biomedical Informatics University of California, San Diego San Diego, CA 92093, USA, lohnomachado@ucsd.edu.
Lucila
L
Ohno-Machado