EVENT : C3BI Seminars
Bioinformatics of structured RNAs beyond energy minimization
Speaker : Yann Ponty, from Computer Science Department (LIX) – École Polytechnique Time : 02:00 pm Starting Date : 24/03/2016
Location : Retrovirus room – LWOFF (22), Institut Pasteur, Paris
Abstract: For the last couple of decades, RNA Bioinformatics has been dedicating much effort to elucidate the sequence-structure relationship in structured non-coding RNAs at the secondary structure level. Quite noticeably, the field has experienced multiple paradigm shifts, transitioning from one-sequence-to-one-structure methods, exemplified by minimum free-energy structure prediction algorithms (MFold), to one-sequence-to-many-structures at the Boltzmann equilibrium (partition function), or postulating kinetic effects, and to many-sequences-to-one/many-structure(s), including comparative folding predicted from multiple homologous sequences. Yet, despite demonstrated improved performances, such methods only slowly permeate applied communities, partly due to their conceptual difficulty and to the absence of centralized tools and standard analysis protocols.
In this talk, I will briefly describe the three main paradigms in RNA Bioinformatics (energy minimization, thermodynamic equilibrium), and mention available state-of-the-art tools for structure prediction. I will mention the relative performances of such tools, and outline an analysis of the results using BRaliBase, the historic benchmark for (comparative) structure prediction. I will conclude with a short tale of benchmark design and interpretation.
Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting