ArticleBioinformatics (Oxford, England)2017
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.International journal of molecular sciences · 2026Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Reference-based read clustering improves theComputational and structural biotechnology journal · 2023Article
- Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation.Nucleic acids research · 2022Article
- Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs.International journal of molecular sciences · 2021Review
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.Algorithms for molecular biology : AMB · 2020Article
- The locality dilemma of Sankoff-like RNA alignments.Bioinformatics (Oxford, England) · 2020Article
- Identification of RNA 3´ ends and termination sites inRNA biology · 2020Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- ShaKer: RNA SHAPE prediction using graph kernel.Bioinformatics (Oxford, England) · 2019Article
- Identification and characterization of novel conserved RNA structures in Drosophila.BMC genomics · 2018Article
- Article
- CMV: visualization for RNA and protein family models and their comparisons.Bioinformatics (Oxford, England) · 2018Article
- Convolutional neural networks for classification of alignments of non-coding RNA sequences.Bioinformatics (Oxford, England) · 2018Article
- Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi.Scientific reports · 2018Article
- SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.PLoS computational biology · 2018Article
- DotAligner: identification and clustering of RNA structure motifs.Genome biology · 2017Article
- Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.BMC genomics · 2017Article
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7 authors.
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Abstract
motivationClustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities. However, existing approaches for clustering paralogous RNAs, do not take the compensatory base pair changes obtained from structure conservation in orthologous sequences into account.
resultsHere, we present RNAscClust , the implementation of a new algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. We show that the clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments. AVAILABILITY AND IMPLEMENTATION: RNAscClust is available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust . CONTACT: gorodkin@rth.dk or backofen@informatik.uni-freiburg.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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