ArticleNucleic acids research2014
Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 52 citations in OpenAlex.
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- RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models.Briefings in bioinformatics · 2024Article
- REDalign: accurate RNA structural alignment using residual encoder-decoder network.BMC bioinformatics · 2024Article
- Using the RNAstructure Software Package to Predict Conserved RNA Structures.Current protocols · 2024Article
- Translational activation by a synthetic PPR protein elucidates control of psbA translation in Arabidopsis chloroplasts.The Plant cell · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- RNA Secondary Structure Analysis Using RNAstructure.Current protocols · 2023Article
- Network-Based Structural Alignment of RNA Sequences Using TOPAS.Methods in molecular biology (Clifton, N.J.) · 2023Article
- In vitro evolution of ribonucleases from expanded genetic alphabets.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses.Viruses · 2022Review
- Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning.NAR genomics and bioinformatics · 2022Article
- aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs.NAR genomics and bioinformatics · 2020Article
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.Algorithms for molecular biology : AMB · 2020Article
- RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference.Molecular therapy. Nucleic acids · 2020Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis.The Plant cell · 2019Article
- Crystal structure of an adenovirus virus-associated RNA.Nature communications · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.