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The relative value of operon predictions

R. W. W. Brouwer, O. P. Kuipers, S. A. F. T. van Hijum
2008 Briefings in Bioinformatics  
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

J. Bockhorst, M. Craven, D. Page, J. Shavlik, J. Glasner
2003 Bioinformatics  
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

N. H. Bergman, K. D. Passalacqua, P. C. Hanna, Z. S. Qin
2006 Applied and Environmental Microbiology  
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

E. Jacob, R. Sasikumar, K. N. R. Nair
2004 Bioinformatics  
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

M.J.L. DE HOON, S. IMOTO, K. KOBAYASHI, N. OGASAWARA, S. MIYANO
2003 Biocomputing 2004  
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

Julia Krushkal, Bin Yan, Laurie N. DiDonato, Marko Puljic, Kelly P. Nevin, Trevor L. Woodard, Ronald M. Adkins, Barbara A. Methé, Derek R. Lovley
2007 Functional & Integrative Genomics  
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

Blanca Taboada, Cristina Verde, Enrique Merino
2010 Nucleic Acids Research  
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

M. N. Price
2005 Nucleic Acids Research  
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

Yogendra Bhaskar, Xiaoquan Su, Chenggang Xu, Jian Xu
2021 Frontiers in Microbiology  
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

Enrique M. Muro, Nancy Mah, Gabriel Moreno-Hagelsieb, Miguel A. Andrade-Navarro
2010 Nucleic Acids Research  
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

Wandaliz Torres-García, Weiwen Zhang, George C. Runger, Roger H. Johnson, Deirdre R. Meldrum
2009 Computer applications in the biosciences : CABIOS  
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

B. P. Westover, J. D. Buhler, J. L. Sonnenburg, J. I. Gordon
2004 Bioinformatics  
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

Amit Sinha, Claudia Langnick, Ralf J. Sommer, Christoph Dieterich
2014 RNA: A publication of the RNA Society  
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

R L Gourse, M Nomura
1984 Journal of Bacteriology  
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

Tessa E.F. Quax, Yuri I. Wolf, Jasper J. Koehorst, Omri Wurtzel, Richard van der Oost, Wenqi Ran, Fabian Blombach, Kira S. Makarova, Stan J.J. Brouns, Anthony C. Forster, E. Gerhart H. Wagner, Rotem Sorek (+2 others)
2013 Cell Reports  
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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