20 research outputs found
A Note on Easy and Efficient Computation of Full Abelian Periods of a Word
Constantinescu and Ilie (Bulletin of the EATCS 89, 167-170, 2006) introduced
the idea of an Abelian period with head and tail of a finite word. An Abelian
period is called full if both the head and the tail are empty. We present a
simple and easy-to-implement -time algorithm for computing all
the full Abelian periods of a word of length over a constant-size alphabet.
Experiments show that our algorithm significantly outperforms the
algorithm proposed by Kociumaka et al. (Proc. of STACS, 245-256, 2013) for the
same problem.Comment: Accepted for publication in Discrete Applied Mathematic
Efficient pattern matching in degenerate strings with the Burrows–Wheeler transform
International audienceA degenerate or indeterminate string on an alphabet Σ is a sequence of non-empty subsets of Σ. Given a degenerate string t of length n, we present a new method based on the Burrows--Wheeler transform for searching for a degenerate pattern of length m in t running in O(mn) time on a constant size alphabet Σ. Furthermore, it is a hybrid pattern-matching technique that works on both regular and degenerate strings. A degenerate string is said to be conservative if its number of non-solid letters is upper-bounded by a fixed positive constant q; in this case we show that the search complexity time is O(qm2). Experimental results show that our method performs well in practice
Practical fast on-line exact pattern matching algorithms for highly similar sequences
International audienc
Fast practical online exact single and multiple pattern matching algorithms in highly similar sequences
International audienceWith the advent of high-throughput sequencing technologies there are more and more genomic sequences of individuals of the same species available. These sequences only differ by a very small amount of variations. There is thus a strong need for efficient algorithms for performing fast pattern matching in such specific sets of sequences. In this paper, we propose efficient practical algorithms that solve on-line exact pattern matching problem in a set of highly similar DNA sequences. We first present a method for exact single pattern matching when k variations are allowed in a window which size is equal to the pattern length. We then propose an algorithm for exact multiple pattern matching when only one variation is allowed in a window which size is equal to the length of the longest pattern. Experimental results show that our algorithms, though not optimal in the worst case, have good performances in practice