ArticleBioinformatics (Oxford, England)2009
De novo computational prediction of non-coding RNA genes in prokaryotic genomes.
Article in Bioinformatics (Oxford, England), 2009. 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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24 citing papers in PubMed, 39 citations in OpenAlex.
- Prevalence of small base-pairing RNAs derived from diverse genomic loci.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.Cell · 2018Article
- An improved method for identification of small non-coding RNAs in bacteria using support vector machine.Scientific reports · 2017Article
- A Review on Recent Computational Methods for Predicting Noncoding RNAs.BioMed research international · 2017Review
- Review
- LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature.PloS one · 2016Article
- Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli.BMC genomics · 2015Article
- Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza.Planta · 2015Article
- Secondary structural entropy in RNA switch (Riboswitch) identification.BMC bioinformatics · 2015Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- The discriminant power of RNA features for pre-miRNA recognition.BMC bioinformatics · 2014Article
- Computational approaches in detecting non- coding RNA.Current genomics · 2013Article
- Predicting sRNAs and their targets in bacteria.Genomics, proteomics & bioinformatics · 2012Review
- Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.Nucleic acids research · 2012Article
- Article
- Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs.BMC genomics · 2012Article
- EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli.BMC research notes · 2011Article
- Genome-wide detection of novel regulatory RNAs in E. coli.Genome research · 2011Article
- The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures.Nucleic acids research · 2011Article
- Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationThe computational identification of non-coding RNA (ncRNA) genes represents one of the most important and challenging problems in computational biology. Existing methods for ncRNA gene prediction rely mostly on homology information, thus limiting their applications to ncRNA genes with known homologues.
resultsWe present a novel de novo prediction algorithm for ncRNA genes using features derived from the sequences and structures of known ncRNA genes in comparison to decoys. Using these features, we have trained a neural network-based classifier and have applied it to Escherichia coli and Sulfolobus solfataricus for genome-wide prediction of ncRNAs. Our method has an average prediction sensitivity and specificity of 68% and 70%, respectively, for identifying windows with potential for ncRNA genes in E.coli. By combining windows of different sizes and using positional filtering strategies, we predicted 601 candidate ncRNAs and recovered 41% of known ncRNAs in E.coli. We experimentally investigated six novel candidates using Northern blot analysis and found expression of three candidates: one represents a potential new ncRNA, one is associated with stable mRNA decay intermediates and one is a case of either a potential riboswitch or transcription attenuator involved in the regulation of cell division. In general, our approach enables the identification of both cis- and trans-acting ncRNAs in partially or completely sequenced microbial genomes without requiring homology or structural conservation. AVAILABILITY: The source code and results are available at http://csbl.bmb.uga.edu/publications/materials/tran/.
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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.