This protocol shows how to detect putative cis-regulatory elements and regions enriched in
such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat …

During the bacterial cell cycle, the processes of chromosome replication, DNA segregation,
DNA repair and cell division are coordinated by precisely defined events. Tremendous …

We discuss recent progresses in computational studies of membrane proteins based on
physical models with parameters derived from bioinformatics analysis. We describe …

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

Using a generalization of the level statistics analysis of quantum disordered systems, we
present an approach able to extract automatically keywords in literary texts. Our approach …

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 …

Alignment-free methods are increasingly used to calculate evolutionary distances between
DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods …

Motivation: The motif discovery problem consists of finding over-represented patterns in a
collection of biosequences. It is one of the classical sequence analysis problems, but still …

Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense
that it raises the question of how essential chromosomal regions are spared from …

This protocol explains how to discover functional signals in genomic sequences by detecting
over-or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the …