ArticleNucleic acids research2011
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- 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
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- Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer.Frontiers in genetics · 2021Review
- Genomic Characterization ofAntibiotics (Basel, Switzerland) · 2020Article
- Rtools: a web server for various secondary structural analyses on single RNA sequences.Nucleic acids research · 2016Article
- A general approach to high-yield biosynthesis of chimeric RNAs bearing various types of functional small RNAs for broad applications.Nucleic acids research · 2015Article
- Rapid production of novel pre-microRNA agent hsa-mir-27b in Escherichia coli using recombinant RNA technology for functional studies in mammalian cells.Drug metabolism and disposition: the biological fate of chemicals · 2014Article
- A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.BMC bioinformatics · 2014Article
- MicroRNA miR-92a-1 biogenesis and mRNA targeting is modulated by a tertiary contact within the miR-17~92 microRNA cluster.Nucleic acids research · 2014Article
- CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.Nucleic acids research · 2013Article
- Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).Journal of computational biology : a journal of computational molecular cell biology · 2012Review
- pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare homologous sequences of the target sequence. We have developed a Web application (CentroidHomfold-LAST) that predicts the secondary structure of the target sequence using automatically collected homologous sequences. LAST, which is a fast and sensitive local aligner, and CentroidHomfold are employed in the Web application. Computational experiments with a commonly-used data set indicated that CentroidHomfold-LAST substantially outperformed conventional secondary structure predictions including CentroidFold and RNAfold.
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