Français Anglais
Accueil Annuaire Plan du site
Accueil > Evenements > Séminaires
Séminaire d'équipe(s) BioInfo
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
Yann Ponty

13 July 2011, 14h00 - 13 July 2011, 15h30
Salle/Bat : 455/PCRI-N
Contact :

Activités de recherche :

Résumé :
Collaboration avec : Jerome Waldispühl, McGill, Montreal, Canada

The analysis of the relationship between sequences and structures (i.e. how mutations affect structures and reciprocally how structures influence mutations) is essential to decipher the principles driving molecular evolution, to infer the origins of genetic diseases or to develop bioengineering applications such as the design of artificial molecules. Because their structures can be predicted from the sequence data only, RNA molecules provide a good framework to study this sequence-structure relationship.
We recently introduced a suite of algorithms called RNAMutants which allows, for the first time, a complete exploration of RNA
sequence-structure maps in polynomial time and space. Formally, RNAMutants takes an input sequence (or seed) to compute the Boltzmann weighted ensembles of mutants with exactly k mutations, and sample mutations from these ensembles.
However, this approach suffers from major limitations. Indeed, since the Boltzmann probabilities of the mutations depend of the free energy of the structures, RNAMutants has difficulties to sample mutant sequences with low GC-contents.

In this talk presented at RECOMB'11, we introduce a novel unbiased adaptive sampling algorithm that enables RNAMutants to sample regions of the
mutational landscape poorly covered by classical algorithms. We applied these methods to sample mutations with low GC-contents. These adaptive sampling techniques can be easily adapted to explore other regions of the sequence and structural landscapes which are difficult to sample. Importantly, these algorithms come at a minimal computational cost.
We demonstrate the insights offered by these techniques on studies of complete RNA sequence structures maps of sizes up to 40 nucleotides. Our results indicate that the GC-content has a strong influence on the size and shape of the evolutionary accessible sequence and structural spaces. In particular, we show that low GC-contents favor the apparition of internal loops and thus possibly the synthesis of tertiary structure motifs. On the other hand, high GC-contents significantly reduce the size of the evolutionary accessible mutational landscapes.

Pour en savoir plus :
Séminaires
A Two-level Auction for Resource Allocation in Mul
Réseaux sans fil et mobiles
Friday 09 March 2018 - 14h30
Salle : 445 - PCRI-N
Mira Morcos .............................................

Binary pattern of length greater than 14 are abeli
Combinatoire
Friday 09 February 2018 - 14h30
Salle : 445 - PCRI-N
Matthieu Rosenfeld .............................................

Approximate Bayesian Computation and Random Forest
Thursday 08 February 2018 - 00h00
Salle : 455 - PCRI-N
Valentin Thouzeau .............................................

A concurrent lock-free algorithm for computing a f
Combinatoire
Friday 12 January 2018 - 14h30
Salle : 445 - PCRI-N
James Mitchell .............................................

Acyclic Partitioning of Large Directed Acyclic Gra
Calcul à haute performance
Tuesday 09 January 2018 - 10h30
Salle : 465 - PCRI-N
Julien Herrmann .............................................