Exactly periodic subspace decomposition based approach for identifying tandem repeats in DNA sequences

The identification and analysis of tandem repeats is an active area of biological and computational research. Tandem repetitive structures in telomeres plays a role in cancer and hyper-variable, trinucleotide tandem repeats are linked to over a dozen major degenerative diseases. They also play a very crucial role in DNA fingerprinting. In this paper we present an algorithm to identify the exact and inexact tandem repeats in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. The algorithm uses a sliding window approach to identify the location of tandem repeats and other patterns that are present in DNA sequence due to repetition of individual nucleotides. Our algorithm also resolves the problems that were present in periodicity explorer algorithm for identifying tandem repeats. The time complexity of the algorithm, when searching for repeats for window size `W' in a DNA sequence S of length N is O(NWlgW). We present some experimental results concerning to sensitivity of our algorithm.