A lightweight Java Applet dedicated to the quick drawing of an RNA secondary structure. VARNA is open-source and distributed under the terms of the GNU GPL license. Automatically scales up and down to take the most out of a limited space. Can draw multiple structures simultaneously. Accepts a wide range of documented and illustrated options, and offers basic user interaction.
A software dedicated to the random generation of sequences. Supports different classes of models, including weighted context-free grammars, Markov models, ProSITE patterns, etc...
A web server that performs three-dimensional alignment and motifs search for experimentally-determined 3D structures of RNA. Takes into account both sequence content, secondary structure (Determined using RNAView), and 3D rotameric properties (Dihedral angles) similarities.
LocalMove addresses the discretization (aka best on-lattice fitting) of 3D macromolecules models, which tries to fit to a discrete (regular) set of points the coordinates of a polymer backbone. Since the problem is notoriously NP-Complete, we implement a local search (Monte Carlo Markov Chain) resolution of the problem based on local moves. Our web server also allows for a wealth of parameters to be set, such as the optimization strategy, the lattice type, the initial configuration...
A Java applet coded as a proof of concept of researches led in collaboration with Mireille Bousquet-Mélou on properties of uni-dimensional walks under various constraints. This piece of software performs a random generation and displays the set of resulting walks that are either unconstrained, positive or culminating on the positive quarter plane, using various algorithmic approaches (Recursive, rejection, Boltzmann sampling ...).
A small JAVA application illustrating a four compression algorithms, unified within a CFG-based framework, analyzed by Lehman and Shelat in their SODA 2002 paper.