Features for computational operon prediction in prokaryotes

Briefings in Functional Genomics

Volumn 11, Issue 4, 2012, Pages 291-299

  Chuang, Li Yeh ^a   Chang, Hsueh Wei ^b   Tsai, Jui Hung ^c   Yang, Cheng Hong ^c  

^a I SHOU UNIVERSITY   (Taiwan)

^b KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^c NATIONAL KAOHSIUNG UNIVERSITY OF APPLIED SCIENCES   (Taiwan)

Author keywords

Algorithm; Operon prediction; Receiver operating characteristic

Indexed keywords

RNA POLYMERASE;

ACCURACY; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; CONSERVATION GENETICS; DATA BASE; DNA SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION; GENE FUSION; GENETIC ALGORITHM; METABOLISM; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; ORTHOLOGY; PHYLOGENY; PREDICTION; PROKARYOTE; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; REGULATOR GENE; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY;

ALGORITHMS; BACILLUS SUBTILIS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, BACTERIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPERON; PHYLOGENY; PROKARYOTIC CELLS; PROMOTER REGIONS, GENETIC; REPRODUCIBILITY OF RESULTS; ROC CURVE; SENSITIVITY AND SPECIFICITY;

EID: 84865127277     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/els024     Document Type: Article

References (59)

1. Jacob E, Sasikumar R, Nair KN. A fuzzy guided genetic algorithm for operon prediction. Bioinformatics 2005;21: 1403-7.
2. Osbourn AE, Field B. Operons. Cell Mol Life Sci 2009;66: 3755-75.
3. Blumenthal T. Operons in eukaryotes. Brief Funct Genomic Proteomic 2004;3:199-211.
4. Joon M, Bhatia S, Pasricha R, et al. Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis. BMCMicrobiol 2010;10:128.
5. Wang S, Wang Y, Du W, et al. A multi-approaches-guided genetic algorithm with application to operon prediction. Artif IntellMed 2007;41:151-9.
6. Pantosti A, Sanchini A, Monaco M. Mechanisms of antibiotic resistance in Staphylococcus aureus. FutureMicrobiol 2007; 2:323-34.
7. Gibson DG, Glass JI, Lartigue C, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010;329:52-6.
8. Sierro N, Makita Y, de Hoon M, et al. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2008;36:D93-6.
9. Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2007;36:D120-4.
10. Wang L, Trawick JD, Yamamoto R, et al. Genome-wide operon prediction in Staphylococcus aureus. Nucleic Acids Res 2004;32:3689-702.
11. Ermolaeva MD, White O, Salzberg SL. Prediction of operons in microbial genomes. Nucleic Acids Res 2001;29: 1216-21.
12. Moreno-Hagelsieb G, Collado-Vides J. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 2002;18:S329-36.
13. Yada T, Nakao M, Totoki Y, et al. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics 1999;15:987-93.
14. Laing E, Sidhu K, Hubbard SJ. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics 2008;9:79.
15. Sabatti C, Rohlin L, Oh MK, et al. Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res 2002;30:2886-93.
16. Bockhorst J, Craven M, Page D, et al. A Bayesian network approach to operon prediction. Bioinformatics 2003;19: 1227-35.
17. Craven M, Page D, Shavlik J, et al. A probabilistic learning approach to whole-genome operon prediction. Proc IntConf Intell SystMol Biol 2000;8:116-27.
18. Westover BP, Buhler JD, Sonnenburg JL, et al. Operon prediction without a training set. Bioinformatics 2005;21: 880-8.
19. de Hoon MJ, Imoto S, Kobayashi K, et al. Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac Symp Biocomput 2004:276-87.
20. Zhang GQ, Cao ZW, Luo QM, et al. Operon prediction based on SVM. Comput Biol Chem 2006;30:233-40
21. Price MN, Huang KH, Alm EJ, et al. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 2005;33:880-92.
22. Li G, Che D, Xu Y. A universal operon predictor for prokaryotic genomes. Bioinformatics Comput Biol 2009;7: 19-38.
23. Edwards MT, Rison SC, Stoker NG, et al. A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. Nucleic Acids Res 2005;33:3253-62.
24. Dam P, Olman V, Harris K, et al. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 2007;35:288-98.
25. Chuang LY, Tsai JH, Yang CH. Binary particle swarm optimization for operon prediction. Nucleic Acids Res 2010; 38:e128.
26. Chen X, Su Z, Dam P, et al. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome.Nucleic Acids Res 2004;32:2147-57.
27. Taboada B, Verde C, Merino E. High accuracy operon prediction method based on STRING database scores. Nucleic Acids Res 2010;38:e130.
28. Mao F, Dam P, Chou J, et al. DOOR: a database for prokaryotic operons. Nucleic Acids Res 2009;37:D459-63.
29. Dehal PS, Joachimiak MP, Price MN, et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res 2010;38:D396-400.
30. Okuda S, Katayama T, Kawashima S, et al. ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res 2006;34:D358-62.
31. Pertea M, Ayanbule K, Smedinghoff M, et al. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res 2008;37:D479-82.
32. Chuang LY, Tsai JH, Yang CH. PPO: predictor for prokaryotic operons. Bioinformatics 2010;26:3127-8.
33. Brouwer RW, Kuipers OP, van Hijum SA. The relative value of operon predictions. Briefings Bioinformatics 2008;9: 367-75.
34. Salgado H, Moreno-Hagelsieb G, Smith TF, et al. Operons in Escherichia coli: genomic analyses and predictions. ProcNatl Acad Sci 2000;97:6652-7.
35. Zheng Y, Szustakowski JD, Fortnow L, et al. Computational identification of operons in microbial genomes. Genome Res 2002;12:1221-30.
36. Kanehisa M, Goto S, Furumichi M, et al. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010;38:D355-60.
37. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631-7.
38. Tatusov RL, Fedorova ND, Jackson JD, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003;4:41.
39. Chen X, Su Z, Xu Y, et al. Computational prediction of operons in Synechococcus sp. WH8102, Genome Inform 2004; 15:211-22.
40. Bockhorst J, Qiu Y, Glasner J, et al. Predicting bacterial transcription units using sequence and expression data. Bioinformatics 2003;19(Suppl 1):i34-43.
41. Cherry JL. Genome size and operon content. J Theor Biol 2003;221:401-10.
42. Pellegrini M, Marcotte EM, Thompson MJ, et al. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999;96: 4285-8.
43. Date SV, Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 2003;21:1055-62.
44. Tamames J, Casari G, Ouzounis C, et al. Conserved clusters of functionally related genes in two bacterial genomes. JMol Evol 1997;44:66-73.
45. Teichmann SA, Babu MM. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol 2002;20:407-10, discussion 10.
46. Guell M, van Noort V, Yus E, et al. Transcriptome complexity in a genome-reduced bacterium. Science 2009; 326:1268-71.
47. Dotsch A, Eckweiler D, Schniederjans M, et al. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoSOne 2012; 7:e31092.
48. Martin J, Zhu W, Passalacqua KD, et al. Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 2010;11(Suppl 3):S10.
49. Toledo-Arana A, Dussurget O, Nikitas G, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 2009;459:950-6.
50. Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010;11:9-16.
51. Mertes F, Elsharawy A, Sauer S, et al. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics 2011;10:374-86.
52. Ludwig M, Bryant DA. Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by next-gen (SOLiD) sequencing of cDNA. FrontMicrobiol 2011;2:41.
53. Giglio S, Chou WK, Ikeda H, et al. Biosynthesis of 2-methylisoborneol in cyanobacteria. Environ Sci Technol 2011;45:992-8.
54. Charaniya S, Mehra S, Lian W, et al. Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor. Nucleic Acids Res 2007;35:7222-36.
55. Tran TT, Dam P, Su Z, et al. Operon prediction in Pyrococcus furiosus. Nucleic Acids Res 2007;35:11-20.
56. Wang PP, Ruvinsky I. Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA 2010;16:290-8.
57. Tjaden B, Saxena RM, Stolyar S, et al. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 2002;30:3732-8.
58. Hanson RK. The development of a brief actuarial risk scale for sexual offense recidivism. Ottawa: Department of the Solicitor General of Canada. (User Report 97-04) 1997.
59. Jensen LJ, Kuhn M, Stark M, et al. STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009