Detection and visualization of tandem repeats in DNA sequences

One conspicuous feature of DNA is the extent to which nucleotide subsequences repeat in the genome. Several strongly repetitive tandem (or contiguous) repeats are known to be associated with genetic diseases, while weaker repetitive structures are thought to be representative of historical events associated with sequence repetition. Thus, it is important to develop sensitive and rapid automation of the detection and identification of repeat sequences. A new algorithm for examining periodic patterns in DNA sequences is developed. The algorithm uses the short-time periodicity transform to compute the closest periodic sequence of fixed length at each nucleotide position in a given sequence to be analyzed. Each such subsequence is then compared to its closest periodic sequence to provide a quantitative measure of the amount of repetition within the sequence. In addition to being used to detect the presence of repeat subsequences in DNA, the periodicity explorer algorithm provides a potentially useful visualization of periodic patterns in a DNA sequence through a graphical display of the relative energy in the optimal periodic projections of the analyzed sequences, i.e., the DNA periodogram. Computationally, the algorithm is linear in the length of the analyzed sequence.