Danny Barash (CS, Ben-Gurion University)
Thursday, 29.11.2012, 13:30
The inverse RNA folding problem for designing sequences that fold into a
given RNA secondary structure was introduced in the early 1990's in Vienna.
Using a coarse-grain tree graph representation of the RNA secondary structure,
we extended the inverse RNA folding problem to include constraints such as
thermodynamic stability and mutational robustness, deveoping a program called
RNAexinv. Furthermore, we propose a fragment-based design approach of RNA
sequences that can be useful to practitioners in a variety of biological
applications. In this shape-based design approach, specific RNA structural
motifs with known biological functions are strictly enforced while others can
possess more flexibility in their structure in favor of preserving physical
attributes and additional constraints.
Detection of RNA thermoswitches and riboswitches in genomic sequences using
structure based methods will also be discussed.
Joint work with Lina Weinbrand, Assaf Avihoo, and Alexander Churkin.