DNA Data Compression Based on the Whole Genome Sequence
Hyoung Do Kim, Ju Han Kim · Journal of Convergence Information Technology · 2009
In order to cope with the rapidly growing genome sequence data, we need a new method for compression. The compression ratios of existing algorithms are just about 1.6 bits per base. Furthermore, it is impossible to compare DNA sequences in their compressed or encoded form. Provided that an anchor point called the whole genome sequence for each organism has been setup in the post genome era, this paper presents a compression method, DNAEncodeWG, based on the whole genome sequence. It finds some regions in the whole genome sequence matching well with a given query sequence and then records the characteristics of the regions and the differences between the two sequences. We have implemented a tool for proving the efficiency and effectiveness of the method.