Computational methods for predicting genomic islands in microbial genomes

Computational and Structural Biotechnology Journal

Volumn 14, Issue , 2016, Pages 200-206

  Lu, Bingxin ^a   Leong, Hon Wai ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Comparative genomics; Genome segmentation; Outlier detection; Pathogenicity islands; Sequence composition

Indexed keywords

COMPUTATIONAL METHODS; FORECASTING; GENE TRANSFER;

ANTIBIOTICS RESISTANCE; COMPARATIVE GENOMICS; GENOME EVOLUTION; GENOME SEGMENTATION; GENOMIC ISLANDS; LATERAL GENE TRANSFERS; MICROBIAL GENOMES; OUTLIER DETECTION; PATHOGENICITY ISLAND; SEQUENCE COMPOSITION;

GENES;

ARTICLE; GENE CLUSTER; GENE SEQUENCE; GENE STRUCTURE; GENOMIC ISLAND; MATHEMATICAL ANALYSIS; MICROBIAL GENOME; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 84971324135     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2016.05.001     Document Type: Short Survey

References (66)

1. H. Ochman, J.G. Lawrence, and E.A. Groisman Lateral gene transfer and the nature of bacterial innovation Nature 405 2000 299 304
2. J.G. Lawrence, and H. Hendrickson Lateral gene transfer: when will adolescence end? Mol Microbiol 50 2003 739 749
3. G.S. Vernikos In Silico Prediction of Genomic Islands in Microbial Genomes 2008 (Ph.D. thesis)
4. J. Sjöstrand, A. Tofigh, V. Daubin, L. Arvestad, J. Sjostrand, and et al. A Bayesian method for analyzing lateral gene transfer Syst Biol 63 2014 409 420
5. J.P. Gogarten, and J.P. Townsend Horizontal gene transfer, genome innovation and evolution Nat Rev Microbiol 3 2005 679 687
6. S.M. Soucy, J. Huang, and J.P. Gogarten Horizontal gene transfer: building the web of life Nat Rev Genet 16 2015 472 482
7. J. Hacker, L. Bender, M. Ott, J. Wingender, B. Lund, and et al. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extra intestinal Escherichia coli isolates Microb Pathog 8 1990 213 225
8. J. Hacker, and J.B. Kaper Pathogenicity islands and the evolution of microbes Annu Rev Microbiol 54 2000 641 679
9. U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker Genomic islands in pathogenic and environmental microorganisms Nat Rev Microbiol 2 2004 414 424
10. M. Juhas, J.R. van der Meer, M. Gaillard, R.M. Harding, D.W. Hood, and et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution FEMS Microbiol Rev 33 2009 376 393
11. X. Bellanger, S. Payot, N. Leblond-Bourget, and G. Guédon Conjugative and mobilizable genomic islands in bacteria: evolution and diversity FEMS Microbiol Rev 38 2014 720 760
12. J. Hacker, G. Blum-Oehler, I. Mühldorfer, and H. Tschäpe Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution Mol Microbiol 23 1997 1089 1097
13. H. Schmidt, and M. Hensel Pathogenicity Islands in bacterial pathogenesis Clin Microbiol Rev 17 2004 14 56
14. K.P. Williams Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies Nucleic Acids Res 30 2002 866 875
15. G.S. Vernikos, and J. Parkhill Resolving the structural features of genomic islands: a machine learning approach Genome Res 18 2008 331 342
16. E.F. Boyd, S. Almagro-Moreno, and P. Ma Genomic islands are dynamic, ancient integrative elements in bacterial evolution Trends Microbiol 17 2009 47 53
17. M.G.I. Langille, W.W.L. Hsiao, and F.S.L. Brinkman Detecting genomic islands using bioinformatics approaches Nat Rev Microbiol 8 2010 373 382
18. J. Hacker, and E. Carniel Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes EMBO Rep 2 2001 376 381
19. S.J. Ho Sui, A. Fedynak, W.W.L. Hsiao, M.G.I. Langille, and F.S.L. Brinkman The association of virulence factors with genomic islands PLoS One 4 2009 e8094
20. D.G. Moriel, I. Bertoldi, A. Spagnuolo, S. Marchi, R. Rosini, and et al. Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli Proc Natl Acad Sci U S A 107 2010 9072 9077
21. D. Che, M.S. Hasan, and B. Chen Identifying pathogenicity islands in bacterial pathogenomics using computational approaches Pathogens 3 2014 36 56
22. S.L. Marcus, J.H. Brumell, C.G. Pfeifer, and B.B. Finlay Salmonella pathogenicity islands: big virulence in small packages Microbes Infect 2 2000 145 156
23. M. Ravenhall, N. Škunca, F. Lassalle, and C. Dessimoz Inferring horizontal gene transfer PLoS Comput Biol 11 2015 e1004095
24. Y. Mantri, and K.P. Williams Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities Nucleic Acids Res 32 2004 D55 D58
25. S.H. Yoon, Y.K. Park, S. Lee, D. Choi, T.K. Oh, and et al. Towards pathogenomics: a web-based resource for pathogenicity islands Nucleic Acids Res 35 2007 D395 D400
26. D. Bi, Z. Xu, E.M. Harrison, C. Tai, Y. Wei, and et al. ICEberg: a web-based resource for integrative and conjugative elements found in bacteria Nucleic Acids Res 40 2012 D621 D626
27. M.G.I. Langille, W.W.L. Hsiao, and F.S.L. Brinkman Evaluation of genomic island predictors using a comparative genomics approach BMC Bioinf 9 2008 329
28. S.H. Yoon, Y.K. Park, and J.F. Kim PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands Nucleic Acids Res 43 2015 D624 D630
29. C.M. Hudson, B.Y. Lau, and K.P. Williams Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes Nucleic Acids Res 43 2015 D48 D53
30. Q. Tu, and D. Ding Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis FEMS Microbiol Lett 221 2003 269 275
31. S. Waack, O. Keller, R. Asper, T. Brodag, C. Damm, and et al. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models BMC Bioinf 7 2006 142
32. G.S. Vernikos, and J. Parkhill Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the salmonella pathogenicity islands Bioinformatics 22 2006 2196 2203
33. I. Rajan, S. Aravamuthan, and S.S. Mande Identification of compositionally distinct regions in genomes using the centroid method Bioinformatics 23 2007 2672 2677
34. R. Chatterjee, K. Chaudhuri, and P. Chaudhuri On detection and assessment of statistical significance of Genomic Islands BMC Genomics 9 2008 150
35. S. Shrivastava, C.V. Siva Kumar Reddy, and S.S. Mande INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms J Biosci 35 2010 351 364
36. B. Lu, and H.W. Leong GI-SVM: a sensitive method for predicting genomic islands based on unannotated sequence of a single genome J Bioinform Comput Biol 14 2016 164003
37. R. Zhang, and C.T.T. Zhang A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I Bioinformatics 20 2004 612 622
38. F. Gao, and C.T. Zhang GC-profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences Nucleic Acids Res 34 2006 W686 W691
39. R. Zhang, H.Y. Ou, F. Gao, and H. Luo Identification of horizontally-transferred Genomic Islands and genome segmentation points by using the GC profile method Curr Genomics 15 2014 113 121
40. A.J. Arvey, R.K. Azad, A. Raval, and J.G. Lawrence Detection of genomic islands via segmental genome heterogeneity Nucleic Acids Res 37 2009 5255 5266
41. W. Hsiao, I. Wan, S.J. Jones, and F.S.L. Brinkman IslandPath: aiding detection of genomic islands in prokaryotes Bioinformatics 19 2003 418 420
42. D. Che, C. Hockenbury, R. Marmelstein, and K. Rasheed Classification of genomic islands using decision trees and their ensemble algorithms BMC Genomics 11 Suppl. 2 2010 S1
43. D. Che, H. Wang, J. Fazekas, and B. Chen An accurate genomic island prediction method for sequenced bacterial and archaeal genomes J Proteomics Bioinform 7 2014 214 221
44. H.Y. Ou, L.L. Chen, J. Lonnen, R.R. Chaudhuri, A.B. Thani, and et al. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria Nucleic Acids Res 34 2006 e3
45. M.G. Langille, and F.S. Brinkman IslandViewer: an integrated interface for computational identification and visualization of genomic islands Bioinformatics 25 2009 664 665
46. B.K. Dhillon, T.A. Chiu, M.R. Laird, M.G.I. Langille, and F.S.L. Brinkman IslandViewer update: improved genomic island discovery and visualization Nucleic Acids Res 41 2013 W129 W132
47. B.K. Dhillon, M.R. Laird, S. Ja, G.L. Winsor, R. Lo, and et al. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis Nucleic Acids Res 43 2015 W104 W108
48. D. Che, M.S. Hasan, H. Wang, J. Fazekas, J. Huang, and et al. EGID: an ensemble algorithm for improved genomic island detection in genomic sequences Bioinformation 7 2011 311 314
49. M.S. Hasan, Q. Liu, H. Wang, J. Fazekas, B. Chen, and et al. GIST: genomic island suite of tools for predicting genomic islands in genomic sequences Bioinformation 8 2012 203
50. S. Pundhir, H. Vijayvargiya, and A. Kumar PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes In Silico Biol 8 2008 223 234
51. S.C. Soares, V.C. Abreu, R.T.J. Ramos, L. Cerdeira, A. Silva, and et al. PIPS: pathogenicity island prediction software PLoS One 7 2012 e30848
52. C.C. Lee, Y.P.P. Chen, T.J. Yao, C.Y. Ma, W.C. Lo, and et al. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects Gene 518 2013 114 123
53. J.G. Lawrence, and H. Ochman Amelioration of bacterial genomes: rates of change and exchange J Mol Evol 44 1997 383 397
54. A. Tsirigos, and I. Rigoutsos A new computational method for the detection of horizontal gene transfer events Nucleic Acids Res 33 2005 922 933
55. R.K. Azad, and J.G. Lawrence Towards more robust methods of alien gene detection Nucleic Acids Res 39 2011 e56
56. S. Karlin Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes Trends Microbiol 9 2001 335 343
57. W.W.L. Hsiao, K. Ung, D. Aeschliman, J. Bryan, B. Brett Finlay, and et al. Evidence of a large novel gene pool associated with prokaryotic genomic islands PLoS Genet 1 2005 e62
58. R. Merkl SIGI: score-based identification of genomic islands BMC Bioinf 5 2004 22
59. S. Garcia-Vallve, E. Guzman, M.A. Montero, and A. Romeu HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes Nucleic Acids Res 31 2003 187 189
60. J. Elhai, H. Liu, and A. Taton Detection of horizontal transfer of individual genes by anomalous oligomer frequencies BMC Genomics 13 2012 245
61. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, and et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 1997 3389 3402
62. A.C.E. Darling, B. Mau, F.R. Blattner, and N.T. Perna Mauve: multiple alignment of conserved genomic sequence with rearrangements Genome Res 14 2004 1394 1403
63. H.Y. Ou, X. He, E.M. Harrison, B.R. Kulasekara, A.B. Thani, and et al. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands Nucleic Acids Res 35 2007 W97 W104
64. S.H. Yoon, C.G. Hur, H.Y. Kang, Y.H. Kim, T.K. Oh, and et al. A computational approach for identifying pathogenicity islands in prokaryotic genomes BMC Bioinf 6 2005 184
65. V. Chandola, A. Banerjee, and V. Kumar Anomaly detection for discrete sequences: a survey IEEE Trans Knowl Data Eng 24 2012 823 839
66. J. Tamames, and A. Moya Estimating the extent of horizontal gene transfer in metagenomic sequences BMC Genomics 9 2008 136