Section: New Results

Noncoding RNAs

• A. Saffarian defended her thesis on November 16. Within her thesis, we obtained two results :

  • We designed a new algorithm to produce all locally optimal secondary structures of an RNA Sequence. Locally optimal secondary structures are thermodynamically stable RNA structures that are maximal for inclusion: they cannot be extended without producing a conflict between base pairs in the secondary structure, or increasing the free energy. A journal article is in revision to Journal of Computational Biology.

  • We also proposed an algorithm to match a multi-structure of RNA against a sequence. A multi-structure gather several RNA structures, as real or putative structures on a same sequence, or as similar structures in a family of RNAs. A journal article was submited to Algorithms for Molecular Biology.

• We published an algorithm for the comparison RNA secondary structures represented as nested arc-annotated sequences [7] .

• The non-coding RNA collaborative annotation platform RNAspace is made available to the community, and published in RNA [3] .