Bioinformatics Advance Access originally published online on May 18, 2006
Bioinformatics 2006 22(15):1823-1831; doi:10.1093/bioinformatics/btl194
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
INFO-RNA—a fast approach to inverse RNA folding
Albert-Ludwigs-University Freiburg, Institute of Computer Science, Chair of Bioinformatics Georges-Koehler-Allee 106, 79110 Freiburg, Germany
*To whom correspondence should be addressed.
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: www.bioinf.uni-freiburg.de?Subpages/software.html
Contact: backofen{at}informatik.uni-freiburg.de
Supplementary information: Supplementary data are available on Bioinformatics online.
Received on March 14, 2006; revised on April 28, 2006; accepted on May 15, 2006
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  A. Busch and R. Backofen INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints Nucleic Acids Res., July 13, 2007; 35(suppl_2): W310 - W313. [Abstract] [Full Text] [PDF]
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