Journal of the ACM (JACM)
Periodic musical sequences and Lyndon words
Soft Computing - A Fusion of Foundations, Methodologies and Applications
STAR: an algorithm to Search for Tandem Approximate Repeats
Bioinformatics
The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching
The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching
Bioinformatics
A four-stage algorithm for updating a Burrows-Wheeler transform
Theoretical Computer Science
Space efficient linear time construction of suffix arrays
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Simple real-time constant-space string matching
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
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In this paper we study Lyndon structures related to the Burrows-Wheeler Transform with potential application to bioinformatics. Next-Generation Sequencing techniques require the alignment of a large set of short reads (between dozens to hundreds of letters) on a reference sequence (millions of letters). The Burrows-Wheeler Transform has been used in various alignment programs which generally compute the Lyndon factorization of the reference sequence as a preprocessing step. We compute the quadratic factorization of all rotations of an input string and the Burrows-Wheeler Transform of a Lyndon substring. From the factored rotations we introduce the Lyndon fountain.