Article

# Alignment of RNA base pairing probability matrices.

Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, Vienna, Austria.

Bioinformatics (Impact Factor: 5.32). 10/2004; 20(14):2222-7. DOI: 10.1093/bioinformatics/bth229 Source: PubMed

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**ABSTRACT:**Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.Availability and Implementation: The software is written in Java 6 (graphical user interface) and C++ (dynamic programming algorithms). The source code and binaries for Linux, Windows and Mac OS are freely available at http://sysbio.uni-ulm.de and are licensed under the GNU GPLv3. hans.kestler@uni-ulm.de.Bioinformatics 09/2013; · 5.47 Impact Factor -
##### Conference Paper: SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

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**ABSTRACT:**Motivation: There is increasing evidence of pervasive transcription, resulting in hundreds of thousands of ncRNAs of unknown function. Standard computational analysis tasks for inferring functional annotations like clustering require fast and accurate RNA comparisons based on sequence and structure similarity. The gold standard for the latter is Sankoff's algorithm [3], which simultaneously aligns and folds RNAs. Because of its extreme time complexity of O(n6), numerous faster "Sankoff-style" approaches have been suggested. Several such approaches introduce heuristics based on sequence alignment, which compromises the alignment quality for RNAs with sequence identities below 60% [1]. Avoiding such heuristics, as e.g. in LocARNA [4], has been assumed to prohibit time complexities better than O(n4), which strongly limits large-scale applications.Proceedings of the 17th international conference on Research in Computational Molecular Biology; 04/2013 -
##### Conference Paper: Exact Pattern Matching for RNA Structure Ensembles

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**ABSTRACT:**ExpaRNA's core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ExpaRNA-P that solves the lifted problem of finding such sets of exact matchings in entire Boltzmann-distributed structure ensembles of two RNAs. Due to a novel kind of structural sparsification, the new algorithm maintains the time and space complexity of the algorithm for fixed input structures. Furthermore, we generalized the chaining algorithm of ExpaRNA in order to compute a compatible subset of ExpaRNA-P's exact matchings. We show that ExpaRNA-P outperforms ExpaRNA in BRAliBase 2.1 benchmarks, where we pass the chained exact matchings as anchor constraints to the RNA alignment tool LocARNA. Compared to LocARNA, this novel approach shows similar accuracy but is six times faster.Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012); 01/2012

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