DNA coding using finite-context models and arithmetic coding

摘要

The interest in DNA coding has been growing with the availability of extensive genomic databases. Although only two bits are sufficient to encode the four DNA bases, efficient lossless compression methods are still needed due to the size of DNA sequences and because standard compression algorithms do not perform well on DNA sequences. As a result, several specific coding methods have been proposed. Most of these methods are based on searching procedures for finding exact or approximate repeats. Low order finite-context models have only been used as secondary, fall back mechanisms. In this paper, we show that finite-context models can also be used as main DNA encoding methods. We propose a coding method based on two finite-context models that compete for the encoding of data, on a block by block basis. The experimental results confirm the effectiveness of the proposed method.