INFO-RNA--a fast approach to inverse RNA folding.

@article{busch-backofen-06, 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.}, address = {Albert-Ludwigs-University Freiburg, Institute of Computer Science, Chair of Bioinformatics Georges-Koehler-Allee 106, 79110 Freiburg, Germany.}, author = {Busch, A. and Backofen, R. }, citeulike-article-id = {890893}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {design}, month = {August}, number = {15}, pages = {1823--1831}, posted-at = {2006-10-10 03:11:23}, priority = {2}, title = {INFO-RNA--a fast approach to inverse RNA folding.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16709587}, volume = {22}, year = {2006} }

TY - JOUR ID - busch-backofen-06 L3 - citeulike-article-id:890893 TI - INFO-RNA--a fast approach to inverse RNA folding. JF - Bioinformatics VL - 22 IS - 15 SP - 1823 EP - 1831 AD - Albert-Ludwigs-University Freiburg, Institute of Computer Science, Chair of Bioinformatics Georges-Koehler-Allee 106, 79110 Freiburg, Germany. SN - 1460-2059 N2 - 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. KW - design AU - Busch, A AU - Backofen, R PY - 2006/08/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16709587 ER -