A survey of techniques for sequence similarities matching in compression

DNA Sequence Compression can be achieved through exploiting the intra-sequence and inter-sequence similarities. In order to have a good compression gain, effective methods have to be used to search for all the similar subsequences within the DNA sequences so that these similar subsequences can be encoded together. Different pattern recognition methods have been used to search for these similar subsequences. They are suffix-based approach, dynamic programming approach, seed extension approach, rule-based approach and parsing approach. A survey of their main ideas and application domains has been given in this paper.