INFO-RNA—a fast approach to inverse RNA folding

• Published in: Bioinformatics Vol. 22; no. 15; pp. 1823 - 1831
• Main Authors: Busch, Anke, Backofen, Rolf
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.08.2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Base Sequence; Bioinformatics; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Chemical; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; RNA - chemistry; RNA - ultrastructure; Sequence Alignment - methods; Sequence Analysis, RNA - methods; Software; Stability; RNA; Refolding; Prediction; Optimization; Original document; Energy; Ordering; Dynamic programming; Structure; Bioinformatics; Distance; Comparative study
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl194

Motivation: The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure. Results: We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor. We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market. Availability: Contact:backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available on Bioinformatics online.