@article{Busch:Backofen:INFO_fast_appro:2006,
author = {Busch, Anke and Backofen, Rolf},
title = {{INFO}-{RNA}--a fast approach to inverse {RNA} folding},
journal = {Bioinformatics},
year = {2006},
doi = {10.1093/bioinformatics/btl194},
volume = {22},
user = {abusch},
pmid = {16709587},
pages = {1823-31},
number = {15},
issn = {1367-4803},
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, 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.}
}