Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
RNA Sequence Design by Reconstruction from Shape and Guiding Observables
The process of designing novel RNA sequences by inverse RNA folding, as implemented in RNAinverse1, can be thought of as a reconstruction of RNA sequences from secondary structure. To link between the inverse RNA folding problem and physical and evolutionary perspectives2, taking into consideration possible observables such as thermodynamic stability, mutational robustness, and linguistic complexity as constraints, an extension of the reconstruction problem was suggested in3 by which the starting point is an RNA shape. Such an extension is justified, for example, in cases where a functional stem-loop structure of a natural sequence should be strictly kept in the designed sequences but a distant motif in the rest of the structure may contain one more or less nucleotide at the expense of another as long as the global shape is preserved. This allows the insertion of physical observables as constraints to the problem, in addition to local sequence and structure rigid ones. In3, the problem was solved by a parallel evolutionary algorithm without considering computational cost. In practice, an efficient method should be developed for a uniprocessor server that solves this problem using an RNAinverse-like approach.
A.A. is partially supported by the Lynn and William Frankel Center for Computer Sciences at Ben-Gurion University.
References and Footnotes
1Department of Computer Science