RNAglib

Python package for RNA 2.5D structures

RNAglib is a Python package built to facilitate data handling, analysis, visualization, and machine learning on RNA 2.5D graphs.

RNAmigos

Prediction of RNA-small molecule binding

RNA modules are conserved 3D fragments of RNA structures. BayesPairing uses a Bayesian network framework to model the modules and predict their occurence in an input sequence.

VeRNAl

Catalog of RNA 3D motifs

RNA modules are conserved 3D fragments of RNA structures. BayesPairing uses a Bayesian network framework to model the modules and predict their occurence in an input sequence.

BayesPairing

Prediction of RNA 3D modules

RNA modules are conserved 3D fragments of RNA structures. BayesPairing uses a Bayesian network framework to model the modules and predict their occurence in an input sequence.

RNA-MoIP

Prediction of RNA 2.5D structures

RNA-MoIP assign structural motifs from the PDB database to secondary structures. It creates a scaffold of that can be used as a template by MC-Sym to generate RNA 3D structures.

aRNhAck

Prediction of nucleotide in binding interface

aRNhAck maps mutational profile (e.g. mutate-and-map SHAPE data) on multiple sequence alignments to predict nucleotides involved in interaction with other molecules (e.g. small molecules or proteins).

IncaRNAtion

Sampling of RNA sequences with target structure

IncaRNAtion in a linear-time algorithm sampling sequences with high-affinity to a target secondary structure.

CaRNAval

CaRNAval is a catalog of RNA 3D motifs that include long-range interactions connecting 2 secondary structure elements (e.g. A-minor motif). These Reccurent Interaction Networks (RINs) are organized in a graphical structure that highlight relationships between them.

ArchARNement

Reconstruction of ancestral RNA sequences

AchARNement analyses an RNA multiple sequence of a clan (i.e. homologous sequences with divergent structures) to predict ancestral sequences. It can uses any phylogenetic tree provided by the user.

RNAmutants

Exploration of RNA sequence-structure maps

RNAmutants explores the complete mutational landscape of an input sequence. It computes the most stable mutants (i.e. with the lowest MFE) or sample mutants with a probability of occurence proportional to their folding energies.

RNApyro

Error-correction of RNA sequencing data

RNApyro fixes errors in sequencing reads of a structured RNA (e.g. 16s rRNA). It calculates mutations of the input sequence that improve the fitness to the target secondary structure.

SPARCS

Analysis of structural content of coding RNA

SPARCS analyzes coding regions of a mRNA sequences to identify positions under selective pressure for structured or unstructured content.

IncaRNAfbinv

Fragment-based design of RNA sequences

IncaRNAfbinv is a tool to design sequences folding into a target secondary structure. It implements a flexible strategy allowing the user to customize the solutions and relax structural constraints.

MateRNAl

Simulation of evolution of RNA populations

MateRNAl is an evolutionary reactor that simulates the evolution of a population of RNA sequences toward target secondary structures or simply toward stable sequences without structural constraints.

Optimol

Optimization of Protein-small molecule binding affinity

P3Fold is a protein folding pathway prediction framework that combines ensemble modelling techniques with evolutionary sequence information method.

P3Fold

Prediction of protein folding routes

P3Fold is a protein folding pathway prediction framework that combines ensemble modelling techniques with evolutionary sequence information method.

Fibrilizer

Analysis of polymorphic Amyloid fibrils

Fibrilizer is suite of tools to build 3D models of polymorphic amyloid structures and compute their energies (including solvation energy). It also features algorithms to explore the mutational landscape.

PartiFold

Prediction of transmembrane β-barrels

PartiFold predict the secondary structures of transmembrane β-barrels and inter-strand residue contact probabilities. It also allows to align two homologous transmembrane β-barrel protein sequences.

DNA Puzzles

Citizen science games in AAA games

DNA puzzles is the code name of our projects in collaboration with game development company. The web page contains blog post about our news and results.

Phylo DNA Puzzles

Citizen science puzzle game for genomics

Phylo DNA puzzles is a tile matching game whose solutions are used to compute accurate DNA multiple sequence alignments. It also features a researcher portal allowing scientits to upload their sequence and an educational site for instructors.

Colony B

Citizen science mobile app for microbiome

Colony B is a mobile game allowing its users to contribute to research on the human microbiome. The solutions collected from the game are used to improve clustering of OTU data.

Market game

A collaborative crowd-computing game

Market is an experimental collaborative game that aims to study how crowds of players collaborate to solve difficult combinatorial problems.

3DGB

Immersive exploration of 3D genomes

3DGB is a lightweight visualization tools of 3D genome structures. It runs in a web browser and allows to study genomic annotations in a 3D environment.

MetaLab

Augmented Experiences for Biofacilities

The MetaLab project aims to explore the potential of augmented/virtual reality and artificial intelligence technologies to enhance user experience in bio-facilities.