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A novel method for accurate operon predictions in all sequenced prokaryotes
- Source :
- Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; & Arkin, Adam P.(2004). A Novel Method for Accurate Operon Predictions in All Sequenced Prokaryotes. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/23p3h2jn, Nucleic Acids Research
- Publication Year :
- 2005
- Publisher :
- Oxford University Press (OUP), 2005.
-
Abstract
- We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83 percent accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacter pylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from six phylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find 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 many operons even though it has unusually wide spacings between conserved adjacent genes.
- Subjects :
- Operon
Pseudogene
Genomics
Bacillus subtilis
Genome
Article
Genetics
RNA, Messenger
Gene
Oligonucleotide Array Sequence Analysis
Models, Statistical
Base Sequence
biology
Gene Expression Profiling
Synechocystis
Computational Biology
Reproducibility of Results
Life Sciences
Prokaryote
biology.organism_classification
Gene expression profiling
Prokaryotic Cells
Operons Comparative Genomics
bacteria
Epsilonproteobacteria
Genome, Bacterial
Pseudogenes
Subjects
Details
- ISSN :
- 13624962
- Volume :
- 33
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....8be1694ea0b2d6ec2e35e44b1db31fa2