ArticleBioinformatics (Oxford, England)2011
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Using the RNAstructure Software Package to Predict Conserved RNA Structures.Current protocols · 2024Article
- Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging.PLoS pathogens · 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
- Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome.NAR genomics and bioinformatics · 2022Article
- rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.Nucleic acids research · 2022Article
- Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses.Viruses · 2022Review
- Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning.Nature communications · 2022Article
- KnotAli: informed energy minimization through the use of evolutionary information.BMC bioinformatics · 2022Article
- LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.BMC bioinformatics · 2022Article
- SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability.Computational and structural biotechnology journal · 2022Article
- LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- Selection of High-Affinity RNA Aptamers That Distinguish between Doxycycline and Tetracycline.Biochemistry · 2020Article
- RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.PloS one · 2020Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Article
- Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.BMC bioinformatics · 2018Article
- TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.Nucleic acids research · 2017Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
motivationWith recent advances in sequencing, structural and functional studies of RNA lag behind the discovery of sequences. Computational analysis of RNA is increasingly important to reveal structure-function relationships with low cost and speed. The purpose of this study is to use multiple homologous sequences to infer a conserved RNA structure.
resultsA new algorithm, called Multilign, is presented to find the lowest free energy RNA secondary structure common to multiple sequences. Multilign is based on Dynalign, which is a program that simultaneously aligns and folds two sequences to find the lowest free energy conserved structure. For Multilign, Dynalign is used to progressively construct a conserved structure from multiple pairwise calculations, with one sequence used in all pairwise calculations. A base pair is predicted only if it is contained in the set of low free energy structures predicted by all Dynalign calculations. In this way, Multilign improves prediction accuracy by keeping the genuine base pairs and excluding competing false base pairs. Multilign has computational complexity that scales linearly in the number of sequences. Multilign was tested on extensive datasets of sequences with known structure and its prediction accuracy is among the best of available algorithms. Multilign can run on long sequences (> 1500 nt) and an arbitrarily large number of sequences. AVAILABILITY: The algorithm is implemented in ANSI C++ and can be downloaded as part of the RNAstructure package at: http://rna.urmc.rochester.edu.
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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.