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

On codes with finite interpreting delay: a defect theorem

We introduce two new classes of codes, namely adjacent codes and codes with finite interpreting delay. For each class, we establish an extension of the defect theorem

Maximal circular codes

We answer to a question of De Luca and Restivo whether there exists a circular code which is maximal as circular code and not as code

A survey of string orderings and their application to the Burrows-Wheeler transform

International audienc

Binary block order Rouen transform

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