ArticleBioinformatics (Oxford, England)2016
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Machine learning for RNA secondary structure prediction: a review of current methods and challenges.RNA (New York, N.Y.) · 2026Review
- Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts.Biology methods & protocols · 2025Article
- REDalign: accurate RNA structural alignment using residual encoder-decoder network.BMC bioinformatics · 2024Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers.Biomedicines · 2024Review
- RNA threading with secondary structure and sequence profile.Bioinformatics (Oxford, England) · 2024Article
- Evolutionary Structure Conservation and Covariance Scores.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction.PLoS computational biology · 2023Article
- Network-Based Structural Alignment of RNA Sequences Using TOPAS.Methods in molecular biology (Clifton, N.J.) · 2023Article
- KnotAli: informed energy minimization through the use of evolutionary information.BMC bioinformatics · 2022Article
- Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning.NAR genomics and bioinformatics · 2022Article
- RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.BMC bioinformatics · 2021Article
- aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs.NAR genomics and bioinformatics · 2020Article
- Structural Alignment and Covariation Analysis of RNA Sequences.Bio-protocol · 2020Article
- RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.PloS one · 2020Article
- Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- The landscape of the non-canonical RNA-binding site of Gemin5 unveils a feedback loop counteracting the negative effect on translation.Nucleic acids research · 2018Article
- DotAligner: identification and clustering of RNA structure motifs.Genome biology · 2017Article
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4 authors.
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Abstract
motivationStructured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing.
resultsTo meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000-6000 nucleotides improve execution up to a factor of five. AVAILABILITY AND IMPLEMENTATION: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign CONTACT: gorodkin@rth.dk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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