Bioinformatics Forum: Fragment-Based Design of RNA sequences and Detection of RNA switches

Danny Barash (CS, Ben-Gurion University)
Thursday, 29.11.2012, 13:30
Taub 701

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.

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