Section: Software and Platforms

Sequence annotation

Participants : François Coste [contact] , Aymeric Antoine-Lorquin, Catherine Belleannée [contact] , Gaëlle Garet, Olivier Quenez, Jacques Nicolas.

We develop tools for discovery and search of complex pattern signatures within biological sequences, with a focus on protein sequences.

Logol Logol is a swiss-army-knife for Pattern matching on DNA/RNA/Protein sequences, using a high-level grammar to permit a large expressivity. Allowed patterns can consist in a combination of motifs, structures (stem-loops, repeats), indels etc. It allows pseudo-knot identification, context sensitive grammatical formalism and full genome analysis. Possible fields of application are the detection of mutated binding sites or stem-loop identification (e.g. in CRISPR (http://crispi.genouest.org/ ) [10] ) [software]

Protomata learner This tool is a grammatical inference framework suitable for learning the specific signature of a functional protein family from unaligned sequences by partial and local multiple alignment and automata modeling. It performs a syntactic characterization of proteins by identification of conservation blocks on sequence subsets and modelling of their succession. Possible fields of application are new members discovery or study (for instance, for site-directed mutagenesis) of, possibly non-homologous, functional families and subfamilies such as enzymatic, signaling or transporting proteins [38] [4] [web server]