ArticleNucleic acids research2004
Genome-wide operon prediction in Staphylococcus aureus.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- DltX ofFrontiers in microbiology · 2017Article
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- Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.Nucleic acids research · 2015Article
- Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria.Molecular microbiology · 2015Article
- Metabolic sensor governing bacterial virulence in Staphylococcus aureus.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Tea tree oil-induced transcriptional alterations in Staphylococcus aureus.Phytotherapy research : PTR · 2013Article
- Opposing roles of σB and σB-controlled SpoVG in the global regulation of esxA in Staphylococcus aureus.BMC microbiology · 2012Article
- Article
- The σB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus.Journal of bacteriology · 2011Article
- Staphylococcus aureus regulates the expression and production of the staphylococcal superantigen-like secreted proteins in a Rot-dependent manner.Molecular microbiology · 2011Article
- Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials.Antimicrobial agents and chemotherapy · 2010Article
- Binary particle swarm optimization for operon prediction.Nucleic acids research · 2010Article
- Operon structure of Staphylococcus aureus.Nucleic acids research · 2010Article
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome.Journal of bacteriology · 2008Article
- Predicting protein linkages in bacteria: which method is best depends on task.BMC bioinformatics · 2008Article
- Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage.BMC genomics · 2008Article
- Late-stage polyribitol phosphate wall teichoic acid biosynthesis in Staphylococcus aureus.Journal of bacteriology · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of operon structure is critical to understanding gene regulation and function, and pathogenesis, and for identifying targets towards the development of new antibiotics in bacteria. Recently, the complete genome sequences of a large number of important human bacterial pathogens have become available for computational analysis, including the major human Gram-positive pathogen Staphylococcus aureus. By annotating the predicted operon structure of the S.aureus genome, we hope to facilitate the exploration of the unique biology of this organism as well as the comparative genomics across a broad range of bacteria. We have integrated several operon prediction methods and developed a consensus approach to score the likelihood of each adjacent gene pair to be co-transcribed. Gene pairs were separated into distinct operons when scores were equal to or below an empirical threshold. Using this approach, we have generated a S.aureus genome map with scores annotated at the intersections of every adjacent gene pair. This approach predicted about 864 monocistronic transcripts and 533 polycistronic operons from the protein-encoding genes in the S.aureus strain Mu50 genome. When compared with a set of experimentally determined S.aureus operons from literature sources, this method successfully predicted at least 91% of gene pairs. At the transcription unit level, this approach correctly identified at least 92% of complete operons in this dataset. This consensus approach has enabled us to predict operons with high accuracy from a genome where limited experimental evidence for operon structure is available.
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