Abstract
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.
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