Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular molecular structure is a common phenomenon in nature, a caveat of the adaptation of alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from super-quadratic to cubic time in the length of the sequences. In this paper, we introduce a new distance measure based on q-grams, and show how it can be applied effectively and computed efficiently for circular sequence comparison. Experimental results, using real DNA, RNA, and protein sequences as well as synthetic data, demonstrate orders-of-magnitude superiority of our approach in terms of efficiency, while maintaining an accuracy very competitive to the state of the art.

A well known result of Fraenkel and Simpson states that the number of distinct squares in a word of length n is bounded by 2n since at each position there are at most two distinct squares whose last occurrence starts. In this paper, we investigate squares in partial words with one hole, or sequences over a finite alphabet that have a “do not know” symbol or “hole”. A square in a partial word over a given alphabet has the form uv where u is compatible with v, and consequently, such square is compatible with a number of words over the alphabet that are squares. Recently, it was shown that for partial words with one hole, there may be more than two squares that have their last occurrence starting at the same position. Here, we prove that if such is the case, then the length of the shortest square is at most half the length of the third shortest square. As a result, we show that the number of distinct squares compatible with factors of a partial word with one hole of length n is bounded by .