Correlogram-Based Method for Comparing Biological Sequences

In this article we have proposed an abstract representation for a sequence using a constant sized 3D matrix. Subsequently the representation may be utilized for many analytical purposes. We have attempted to use it for comparing sequences, and analyzed the method's asymptotic complexity. Providing a metric for sequence comparison is an underlying operation to many bioinformatics applications. In order to show the effectiveness of the proposed sequence comparison technique we have generated some phylogeny over two sets of bio-sequences and compared them with the ones available in literature. The results prove that our technique is comparable to the standard ones. The technique, called the correlogram-based method, is borrowed from the image analysis area. We have also done some experiments with synthetically generated sequences in order to compare correlogram-based method with the well-known dynamic programming method. Finally, we have discussed some other possibilities on how our method can be used or extended.