Investigating the RFAM paradox: The pseudoknot explanation

Stefan Janssen (1) , Yann Ponty (2, 3) , Balaji Raman (2, 3) , Saad Sheikh (2, 3) , Jean-Marc Steyaert (3, 2) , Peter Clote (3, 4)

1 Faculty of Technology
2 AMIB - Algorithms and Models for Integrative Biology
3 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
4 Department of Biology

In this short note, we investigate the responsibility of pseudoknotted (PK) foldings in the observed incapacity of an MFE folding method (RNAfold) to predict the structure of certain families of RNA within RFam. We considered the difference Delta in predicted free-energy obtained by respectively considering and omitting PK conformations, which we showed could be reliably used as an indicator for the presence of pseudoknots (84.5% AUC, while 88.3% of PK families have positive values). We furthered our analysis, investigating the top 15 families associated with positive values of Delta associated with non-PK consensus structures in RFAM, and found evidence of the presence of PK in the literature for at least 11 of them. However a large proportion of poorly predicted families remain associated with low Delta values, and additional explanations need be explored for their poor predictions.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Stefan Janssen, Yann Ponty, Balaji Raman, Saad Sheikh, Jean-Marc Steyaert, et al.. Investigating the RFAM paradox: The pseudoknot explanation. Fifth Indo-French Bioinformatics Meeting, Mar 2011, Hyderabad, India. ⟨hal-00585647⟩