Algorithm for DNA sequence compression based on prediction of mismatch bases and repeat location
Kalyan Kumar Kaipa, Ajit S. Bopardikar, Srikantha Abhilash, Parthasarathy Venkataraman, Kyusang Lee, TaeJin Ahn, Rangavittal Narayanan · 2010
For DNA sequence Compression, it has been observed that methods based on Markov modeling and repeats give best results. However, these methods tend to use uniform distribution assumption of mismatches for approximate repeats. We show that these replacements are not uniformly distributed and we can improve compression efficiency by using non uniform distribution for mismatches. We also propose a hash table based method to predict repeat location which works well for block based genomic sequence compression algorithms. The proposed methods give good compression gains. The method can be incorporated into any algorithm that uses approximate repeats to realize similar gains.