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Bioinformatics Advance Access published online on May 18, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl194
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© 2006 The Author(s)
Received March 14, 2006
Revised April 28, 2006
Accepted May 15, 2006

Article

INFO-RNA - a fast approach to inverse RNA folding

Anke Busch 1 and Rolf Backofen 1 *

1 Albert-Ludwigs-University Freiburg, Institute of Computer Science, Chair of Bioinformatics, Georges-Koehler-Allee 106, 79110 Freiburg, Germany

* To whom correspondence should be addressed.
Rolf Backofen, E-mail: backofen{at}informatik.uni-freiburg.de


  Abstract

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, that 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.

Associate Editor: Martin Bishop
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Home page
 Nucleic Acids ResHome page
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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