Journal ArticleDOI
A universal operon predictor for prokaryotic genomes.
Guojun Li,Dongsheng Che,Ying Xu +2 more
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TLDR
A novel operon prediction method that is applicable to any prokaryotic genome with high prediction accuracy and has higher prediction sensitivity as well as specificity than most of the published methods.Abstract:
Identification of operons at the genome scale of prokaryotic organisms represents a key step in deciphering of their transcriptional regulation machinery, biological pathways, and networks. While numerous computational methods have been shown to be effective in predicting operons for well-studied organisms such as Escherichia coli K12 and Bacillus subtilis 168, these methods generally do not generalize well to genomes other than the ones used to train the methods, or closely related genomes because they rely on organism–specific information. Several methods have been explored to address this problem through utilizing only genomic structural information conserved across multiple organisms, but they all suffer from the issue of low prediction sensitivity. In this paper, we report a novel operon prediction method that is applicable to any prokaryotic genome with high prediction accuracy. The key idea of the method is to predict operons through identification of conserved gene clusters across multiple genomes and through deriving a key parameter relevant to the distribution of intergenic distances in genomes. We have implemented this method using a graph-theoretic approach, to calculate a set of maximum gene clusters in the target genome that are conserved across multiple reference genomes. Our computational results have shown that this method has higher prediction sensitivity as well as specificity than most of the published methods. We have carried out a preliminary study on operons unique to archaea and bacteria, respectively, and derived a number of interesting new insights about operons between these two kingdoms. The software and predicted operons of 365 prokaryotic genomes are available at .read more
Citations
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Journal ArticleDOI
High accuracy operon prediction method based on STRING database scores
TL;DR: A simple and highly accurate computational method based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database, which was successfully tested on the set of experimentally defined operons in E. coli and B. subtilis.
Journal ArticleDOI
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli
TL;DR: A computational study of the landscape of the transcriptional units (TUs) of E. coli K12 reveals that different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic sequence.
Journal ArticleDOI
Binary particle swarm optimization for operon prediction
TL;DR: A binary particle swarm optimization method is used for operon prediction in bacterial genomes to predict operons with high accuracy for these three genomes, for which only limited data on the properties of the operon structure exists.
Journal ArticleDOI
Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing
TL;DR: This review provides an outline of these powerful tools and the in silico analyses used in their application, and also highlights the biological questions being addressed in these approaches.
Journal ArticleDOI
Computational operon prediction in whole-genomes and metagenomes.
TL;DR: Advances in sequencing technologies and development of better analysis methods will help researchers to overcome the technological hurdles and further improve operon predictions and better utilize operonic information.
References
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Journal ArticleDOI
Conserved domains in DNA repair proteins and evolution of repair systems
TL;DR: Several additional general trends in the evolution of repair proteins were noticed; in particular, multiple, independent fusions of helicase and nuclease domains, and independent inactivation of enzymatic domains that apparently retain adaptor or regulatory functions.
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A novel method for accurate operon predictions in all sequenced prokaryotes
TL;DR: This work combines comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes, and finds several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has manyOperon structure across 124 genomes.
Journal ArticleDOI
A global analysis of Caenorhabditis elegans operons
Thomas Blumenthal,Donald Evans,Christopher D. Link,Alessandro Guffanti,Daniel Lawson,Jean Thierry-Mieg,Danielle Thierry-Mieg,Wei Lu Chiu,Kyle Duke,Moni Kiraly,Stuart K. Kim +10 more
TL;DR: The evidence indicates that the genome contains at least 1,000 operons, 2–8 genes long, that contain about 15% of all C. elegans genes, and inspection of the operon list should reveal previously unknown functional relationships.
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Operons in Escherichia coli: genomic analyses and predictions.
TL;DR: The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of functional relationships of adjacent genes in the same operon, as opposed to adjacent gene in different transcription units.