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The relative value of operon predictions
2008
Briefings in Bioinformatics
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Here, we survey the current status of operon prediction methods. ...
For most organisms, computational operon predictions are the only source of genome-wide operon information. ...
Acknowledgements This work is part of the BioRange programme of the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI ...
doi:10.1093/bib/bbn019
pmid:18420711
fatcat:lqisclufbvdo7bnhs5b2qxw4xm
A Bayesian network approach to operon prediction
2003
Bioinformatics
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We evaluate our approach on the Escherichia coli K-12 genome where our results indicate we are able to identify over 78% of its operons at a 10% false positive rate. ...
Motivation: In order to understand transcription regulation in a given prokaryotic genome, it is critical to identify operons, the fundamental units of transcription, in such species. ...
We perform this analysis to determine the relative value of the data sources and the predictive value of our approach under conditions of reduced data sources. ...
doi:10.1093/bioinformatics/btg147
pmid:12835266
fatcat:i4waqd2hgrhqnjgrufl24pkuou
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information
2006
Applied and Environmental Microbiology
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Overall, our findings show that this algorithm is capable of highly sensitive and accurate operon prediction in a wide range of bacterial genomes and that these predictions can lead to the rapid discovery ...
In this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a Bayesian hidden Markov model that incorporates comparative genomic data with ...
ACKNOWLEDGMENTS We gratefully acknowledge Nathan Fisher and other members of the Hanna lab for useful discussions. This work was supported by DHHS contract N266200400059C/N01-AI-40059. ...
doi:10.1128/aem.01686-06
pmid:17122389
pmcid:PMC1800777
fatcat:zz3zswuyonckpegifdfrpby44q
A fuzzy guided genetic algorithm for operon prediction
2004
Bioinformatics
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Method: A genetic algorithm is developed to evolve a starting population of putative operon maps of the genome into progressively better predictions. ...
Motivation: The operon structure of the prokaryotic genome is a critical input for the reconstruction of regulatory networks at the whole genome level. ...
ACKNOWLEDGEMENTS We wish to express our thanks to Ms Yamuna Devi and Mr Jijoy Joseph for helping with the preparation of the data files. Our sincere gratitude to Prof. ...
doi:10.1093/bioinformatics/bti156
pmid:15564303
fatcat:36y22uwqfvam5blqoeajmlegey
PREDICTING THE OPERON STRUCTURE OF BACILLUS SUBTILIS USING OPERON LENGTH, INTERGENE DISTANCE, AND GENE EXPRESSION INFORMATION
2003
Biocomputing 2004
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The discriminant value for the Bayesian classifier can be chosen by considering the associated cost of misclassifying an operon or a nonoperon gene pair. ...
We predict the operon structure of the Bacillus subtilis genome using the average operon length, the distance between genes in base pairs, and the similarity in gene expression measured in time course ...
Acknowledgments We would like to thank Yuko Makita and Mitsuteru Nakao of the University of Tokyo for assisting us with the σ A and terminator sequence motif prediction. ...
doi:10.1142/9789812704856_0027
fatcat:b5skp3bxfvdvti3wbituqy2swi
Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant
2007
Functional & Integrative Genomics
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Rel Gsu is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. ...
Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur-and RpoS-regulated sites. ...
This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No. DE-FC02-02ER63446. ...
doi:10.1007/s10142-007-0048-5
pmid:17406915
fatcat:7nm4tnsojnctnp4zsciwbvvanm
High accuracy operon prediction method based on STRING database scores
2010
Nucleic Acids Research
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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 ...
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. ...
the manuscript. ...
doi:10.1093/nar/gkq254
pmid:20385580
pmcid:PMC2896540
fatcat:f5taehnbfzan5cjadfix543ckm
A novel method for accurate operon predictions in all sequenced prokaryotes
2005
Nucleic Acids Research
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We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. ...
are more accurate than distance-only predictions trained on a database of E.coli transcripts. ...
rest of the Arkin lab for comments on the manuscript. ...
doi:10.1093/nar/gki232
pmid:15701760
pmcid:PMC549399
fatcat:r3ekibl3abfctl274qnbjebeye
Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp
2021
Frontiers in Microbiology
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stoichiometry of the operon. ...
The ability to identify genome-wide SRPS operons and predict their stoichiometry via DNA sequence in silico should facilitate studying the function and evolution of SRPS operons in bacteria. ...
Inset: average correlation values for the two categories of operons. the SLOFE-predicted ratio and the transcript level. ...
doi:10.3389/fmicb.2021.673349
pmid:34177856
pmcid:PMC8219983
fatcat:sfa3wmtrkzbxfadhv4o5xpo54y
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons
2010
Nucleic Acids Research
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We observed that both tend to be located in the 3 0 (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). ...
In a complementary analysis, we found a significant tendency for essential genes to be located at the 5 0 (upstream) half of the operon (P-value of 0.006). ...
ACKNOWLEDGEMENTS The authors thank Francisco Alonso-Sanchez (CSIC, Madrid, Spain) for helpful discussions and the anonymous referees for their comments. ...
doi:10.1093/nar/gkq1067
pmid:21051341
pmcid:PMC3061063
fatcat:ujimey7rvba4blpxyraxd6xg24
Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins
2009
Computer applications in the biosciences : CABIOS
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Initially, we constructed a GBT model using all possible variables to assess their relative importance and characterize the behavior of the predictive model. ...
of variation of estimated protein abundance values within operons, regulons or pathways are indeed smaller than those for random groups of proteins. ...
Funding: The work is supported by the National Human Genome Research Institute (NHGRI) Center of Excellence in Genomic Sciences (Grant No. 5 P50 HG002360) of the National Institutes of Health (NIH). ...
doi:10.1093/bioinformatics/btp325
pmid:19447782
pmcid:PMC2712339
fatcat:rs76ryydhzg6njdfv6ppmrco7q
Operon prediction without a training set
2004
Bioinformatics
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Figures 1, 2 , and 3 respectively show the effects of changes to β, τ , and ψ. Operon finder performance was relatively insensitive to parameter changes over the ranges tested. ...
To determine whether our parameter choices were appropriate, we investigated the effects of changing these values on the performance of the classifier in E. coli . ...
Figures 1, 2 , and 3 respectively show the effects of changes to β, τ , and ψ. Operon finder performance was relatively insensitive to parameter changes over the ranges tested. ...
doi:10.1093/bioinformatics/bti123
pmid:15539453
fatcat:suxupwaktjesxekezwv6x25qna
Genome-wide analysis oftrans-splicing in the nematodePristionchus pacificusunravels conserved gene functions for germline and dauer development in divergent operons
2014
RNA: A publication of the RNA Society
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We could confirm 2219 operons by RNA-seq data out of 6709 candidate operons, which were predicted by sequence information alone. ...
To see whether the content or organization of operons serves similar roles across species, we experimentally defined operons in the nematode model Pristionchus pacificus. ...
This study was partially funded by the Federal Ministry for Education and Research (BMBF) and the Senate of Berlin, Berlin, Germany (grant to C.D.). Author ...
doi:10.1261/rna.041954.113
pmid:25015138
pmcid:PMC4138322
fatcat:yo4x33pgareadmeslc365vcaa4
Level of rRNA, not tRNA, synthesis controls transcription of rRNA and tRNA operons in Escherichia coli
1984
Journal of Bacteriology
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From the results obtained, we conclude that neither the tRNAs encoded within rRNA operons nor the tRNAs encoded in non-rRNA operons are capable of controlling rRNA or tRNA transcription. ...
In this paper, we examined the following questions. (i) Are the spacer tRNAs carried within rRNA operons the products responsible for the regulation of rRNA and tRNA transcription? ...
Hoffman for preparation of the manuscript. ...
pmid:6094496
pmcid:PMC215812
fatcat:oohpvmdiprbkpgsewe5aklxdwu
Differential Translation Tunes Uneven Production of Operon-Encoded Proteins
2013
Cell Reports
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A threshold value of 0.02 for the family average value DF was determined to minimize the error rate for the prediction of highstoichiometry subunits, resulting in a prediction accuracy of 96% for the analyzed ...
(B) Predicted mRNA folding energy (DE) of the RBS region of each cistron (À20 to +20 bp relative to the start codon). ...
doi:10.1016/j.celrep.2013.07.049
pmid:24012761
fatcat:7kzolbalmnfklgt5oaaggqkz4i
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