Motivation: Alignment-free methods for sequence comparison are increasingly used for
genome analysis and phylogeny reconstruction; they circumvent various difficulties of …

Motivation: Alignment-based methods for sequence analysis have various limitations if large
datasets are to be analysed. Therefore, alignment-free approaches have become popular in …

In this article, we present a user-friendly web interface for two alignment-free sequence-
comparison methods that we recently developed. Most alignment-free methods rely on exact …

Motivation K-mer-based methods are used ubiquitously in the field of computational biology.
However, determining the optimal value of k for a specific application often remains …

Alignment-free methods are one of the mainstays of biological sequence comparison, ie, the
assessment of how similar two biological sequences are to each other, a fundamental and …

In this paper we address the problem of state encoding for synchronous finite state
machines. The primary goal is the reduction of switching activity in the state register. At the …

Spaced seeds have been recently shown to not only detect more alignments, but also to
give a more accurate measure of phylogenetic distances, and to provide a lower …

With the exponential growth of sequence information stored over the last decade, including
that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric …

Vectoral and alignment-free approaches to biological sequence representation have been
explored in bioinformatics to efficiently handle big data. Even so, most current methods …

Motivation Most methods for pairwise and multiple genome alignment use fast local
homology search tools to identify anchor points, ie high-scoring local alignments of the input …