Discovering Frequent Poly-Regions in DNA Sequences

The problem of discovering arrangements of regions of high occurrence of one or more items of a given alphabet in a sequence, is studied, and two efficient approaches are proposed to solve it. The first approach is entropy-based and uses an existing recursive segmentation technique to split the input sequence into a set of homogeneous segments. The key idea of the second approach is to use a set of sliding windows over the sequence. Each sliding window keeps a set of statistics of a sequence segment that mainly includes the number of occurrences of each item in that segment. Combining these statistics efficiently yields the complete set of regions of high occurrence of the items of the given alphabet. After identifying these regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a region). An efficient algorithm for mining frequent arrangements of temporal intervals on a single sequence is applied on the converted sequence to discover frequently occurring arrangements of these regions. The proposed algorithms are tested on various DNA sequences producing results with potentially significant biological meaning.