ArticleNucleic acids research2010
High accuracy operon prediction method based on STRING database scores.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Analysis and comparison of the bacterial σ54 regulon: Evidence of phylogenetic trends in gene regulation.PloS one · 2025Article
- OpDetect: A convolutional and recurrent neural network classifier for precise and sensitive operon detection from RNA-seq data.PloS one · 2025Article
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- Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism.Microbial biotechnology · 2024Article
- Disorder and amino acid composition in proteins: their potential role in the adaptation of extracellular pilins to the acidic media, where Acidithiobacillus thiooxidans grows.Extremophiles : life under extreme conditions · 2023Article
- The Azotobacter vinelandii AlgU regulon during vegetative growth and encysting conditions: A proteomic approach.PloS one · 2023Article
- Antisense-acting riboswitches: A poorly characterized yet important model of transcriptional regulation in prokaryotic organisms.PloS one · 2023Article
- Proteome-wide analysis of lysine 2-hydroxyisobutyrylation in Frankliniella occidentalis.BMC genomics · 2022Article
- Current and Emerging Tools of Computational Biology To Improve the Detoxification of Mycotoxins.Applied and environmental microbiology · 2022Article
- Detecting operons in bacterial genomes via visual representation learning.Scientific reports · 2021Article
- Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons.BMC genomics · 2021Article
- STING controls intestinal homeostasis through promoting antimicrobial peptide expression in epithelial cells.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- A computational system for identifying operons based on RNA-seq data.Methods (San Diego, Calif.) · 2020Review
- Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis.International ophthalmology · 2020Article
- Structure and Evolution ofFrontiers in microbiology · 2020Article
- The actinobacterium Tsukamurella paurometabola has a functionally divergent arylamine N-acetyltransferase (NAT) homolog.World journal of microbiology & biotechnology · 2019Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,A., Simonovic,M. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416). These two parameters were used to train a neural network on a subset of experimentally characterized Escherichia coli and Bacillus subtilis operons. Our predictive model was successfully tested on the set of experimentally defined operons in E. coli and B. subtilis, with accuracies of 94.6 and 93.3%, respectively. As far as we know, these are the highest accuracies ever obtained for predicting bacterial operons. Furthermore, in order to evaluate the predictable accuracy of our model when using an organism's data set for the training procedure, and a different organism's data set for testing, we repeated the E. coli operon prediction analysis using a neural network trained with B. subtilis data, and a B. subtilis analysis using a neural network trained with E. coli data. Even for these cases, the accuracies reached with our method were outstandingly high, 91.5 and 93%, respectively. These results show the potential use of our method for accurately predicting the operons of any other organism. Our operon predictions for fully-sequenced genomes are available at http://operons.ibt.unam.mx/OperonPredictor/.
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