Abstract
A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to locate all the tandem repeats in a weighted sequence. A repeated substring is called a tandem repeat if each occurrence of the substring is directly adjacent to each other. By introducing the idea of equivalence classes in weighted sequences, we identify the tandem repeats of every possible length using an iterative partitioning technique. We also present the algorithm for recording the tandem repeats, and prove that the problem can be solved in O(n2) time.
Highlights
A weighted biological sequence, called for short a weighted sequence, is a special string that allows a set of characters to occur at each position of the sequence with respective probability, instead of a fixed single character occurring in a normal string
We present our algorithm for computing all the tandem repeats in weighted sequences, and give experimental results to verify the algorithm’s performance
The paper investigated the tandem repeats arisen in weighted sequences
Summary
A weighted biological sequence, called for short a weighted sequence, is a special string that allows a set of characters to occur at each position of the sequence with respective probability, instead of a fixed single character occurring in a normal string. A factor f of a weighted sequence X is called a repeat in X if there exist at least two distinct positions of X that are occurrences of f in X. Definition 2 A factor f of length p of a weighted sequence X is called a tandem repeat in X if there exists a triple (i, f, l) such that for each 0 ≤ j
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