My Face
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Yann Ponty - CR CNRS@LIX
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 ...).
Grammar-based compression - [dedicated page French flag] [Reference]
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.
Copyleft Yann Ponty 2015