ArticleBioinformatics (Oxford, England)2012
GraphClust: alignment-free structural clustering of local RNA secondary structures.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.International journal of molecular sciences · 2026Article
- isoTar: miRNA-Target Consensus Prediction with Enrichment Analysis for Canonical and Modified miRNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts.Biology methods & protocols · 2025Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.Briefings in bioinformatics · 2023Review
- RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.Computational 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
- Prediction and analysis of functional RNA structures within the integrative genomics viewer.NAR genomics and bioinformatics · 2022Article
- Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning.NAR genomics and bioinformatics · 2022Article
- Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations.Briefings in bioinformatics · 2021Article
- Mapping the RNA structural landscape of viral genomes.Methods (San Diego, Calif.) · 2020Article
- Augmented base pairing networks encode RNA-small molecule binding preferences.Nucleic acids research · 2020Article
- A comprehensive survey of integron-associated genes present in metagenomes.BMC genomics · 2020Article
- Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs.Frontiers in microbiology · 2020Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.Methods (San Diego, Calif.) · 2019Review
- isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Convolutional neural networks for classification of alignments of non-coding RNA sequences.Bioinformatics (Oxford, England) · 2018Article
- aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationClustering according to sequence-structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs.
resultsWe present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence-structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. AVAILABILITY: The GraphClust pipeline is available on request.
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