An index for a finite automaton is a powerful data structure that supports locating paths
labeled with a query pattern, thus solving pattern matching on the underlying regular …

For the first time we provide a succinct pattern matching index for arbitrary graphs that can
be built in polynomial time, while improving both space and query time bounds from SODA …

Presenting the fundamental algorithms and data structures that power bioinformatics
workflows, this book covers a range of topics from the foundations of sequence analysis …

The problem of aligning a sequence to a walk in a labeled graph is of fundamental
importance to Computational Biology. For an arbitrary graph G=(V, E) and a pattern P of …

The states of a finite-state automaton 𝒩 can be identified with collections of words in the
prefix closure of the regular language accepted by 𝒩. But words can be ordered, and among …

Matching statistics were introduced to solve the approximate string matching problem, which
is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al.[SPIRE …

Wheeler nondeterministic finite automata (WNFAs) were introduced as a generalization of
prefix sorting from strings to labeled graphs. WNFAs admit optimal solutions to classic hard …

In recent years, several compressed indexes based on variants of the Burrows–Wheeler
transform have been introduced. Some of these are used to index structures far more …

The problem of String Matching to Labeled Graphs (SMLG) asks to find all the paths in a
labeled graph $ G=(V, E) $ whose spellings match that of an input string $ S\in\Sigma^ m …

Introduced about thirty years ago in the field of data compression, the Burrows-Wheeler
Transform (BWT) is a string transformation that, besides being a booster of the performance …