ArticleNucleic acids research2005
A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 88 citations in OpenAlex.
- Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.mSystems · 2022Article
- OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.PLoS computational biology · 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
- The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.Microorganisms · 2020Article
- Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays).The plant genome · 2020Article
- A study on multi-omic oscillations in Escherichia coli metabolic networks.BMC bioinformatics · 2018Article
- Transcriptome dynamics-based operon prediction in prokaryotes.BMC bioinformatics · 2014Article
- Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.Molecular & cellular proteomics : MCP · 2011Article
- Article
- Binary particle swarm optimization for operon prediction.Nucleic acids research · 2010Article
- High accuracy operon prediction method based on STRING database scores.Nucleic acids research · 2010Article
- Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.Genome research · 2009Article
- High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.BMC genomics · 2008Article
- Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis.Microbiology (Reading, England) · 2007Article
- Operon prediction using both genome-specific and general genomic information.Nucleic acids research · 2007Article
- Operon prediction in Pyrococcus furiosus.Nucleic acids research · 2007Article
- MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria.BMC bioinformatics · 2006Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli.
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