A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison

Abstract

We present a lossless compression algorithm, GenCompress, for genetic sequences, based on searching for approximate repeats. Our algorithm achieves the best compression ratios for benchmark DNA sequences. Significantly better compression results show that the approximate repeats are one of the main hidden regularities in DNA sequences.
We then describe a theory of measuring the relatedness between two DNA sequences. Using our algorithm, we present strong experimental support for this theory, and demonstrate its application in comparing genomes and constructing evolutionary trees.