Software
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...
Web servers
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...
Misc
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 ...).
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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.