Enhanced annotations and features for comparing thousands of Pseudomonasgenomes in the Pseudomonas genome database

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D646-D653

  Winsor, Geoffrey L ^a   Griffiths, Emma J ^a   Lo, Raymond ^a   Dhillon, Bhavjinder K ^a   Shay, Julie A ^a   Brinkman, Fiona S L ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOINFORMATICS; CELLULAR DISTRIBUTION; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER PREDICTION; CURATED GENOME ANNOTATION; DATA ANALYSIS; EVOLUTIONARY HOMOLOGY; GENE; GENE ONTOLOGY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC VARIATION; GENOME ASSEMBLY; GENOMIC ISLAND; INFORMATION SYSTEM; MOLECULAR GENETICS; NONHUMAN; ORTHOLOGY; PATHOGEN ASSOCIATED GENE; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS GENOME DATABASE; RNA SEQUENCE; THREE DIMENSIONAL IMAGING; WEB BROWSER; ANTIBIOTIC RESISTANCE; CHEMISTRY; DRUG EFFECTS; GENETICS; INTERNET; PATHOGENICITY;

BACTERIAL PROTEIN; VIRULENCE FACTOR;

BACTERIAL PROTEINS; DATABASES, GENETIC; DRUG RESISTANCE, BACTERIAL; GENE ONTOLOGY; GENOME, BACTERIAL; GENOMIC ISLANDS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PSEUDOMONAS; VIRULENCE FACTORS;

EID: 84976908656     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1227     Document Type: Article

References (44)

1. Mathee, K., Narasimhan, G., Valdes, C., Qiu, X., Matewish, J.M., Koehrsen, M., Rokas, A., Yandava, C.N., Engels, R., Zeng, E. et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. U. S. A., 105, 3100-3105.
2. Klockgether, J., Cramer, N., Wiehlmann, L., Davenport, C.F. and Tummler, B. (2011) Pseudomonas aeruginosa genomic structure and diversity. Front. Microbiol., 2, 150.
3. Winsor, G.L., Lam, D.K., Fleming, L., Lo, R., Whiteside, M.D., Yu, N.Y., Hancock, R.E. and Brinkman, F.S. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res., 39, D596-D600.
4. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S., Hufnagle, W.O., Kowalik, D.J., Lagrou, M. et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406, 959-964.
5. Brinkman, F.S., Hancock, R.E. and Stover, C.K. (2000) Sequencing solution: use volunteer annotators organized via internet. Nature, 406, 933.
6. Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
7. Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236-1240.
8. Chibucos, M.C., Mungall, C.J., Balakrishnan, R., Christie, K.R., Huntley, R.P., White, O., Blake, J.A., Lewis, S.E. and Giglio, M. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford), 2014, doi:10.1093/database/bau075.
9. Chen, L., Xiong, Z., Sun, L., Yang, J. and Jin, Q. (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res., 40, D641-D645.
10. Xiang, Z., Tian, Y. and He, Y. (2007) PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol., 8, R150.
11. Yu, N.Y., Wagner, J.R., Laird, M.R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S.C., Ester, M., Foster, L.J. et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26, 1608-1615.
12. Rose, P.W., Prlic, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J.D., Woo, J. et al. (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res., 43, D345-D356.
13. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
14. Pundir, S., Magrane, M., Martin, M.J., O'Donovan, C. and UniProt Consortium. (2015) Searching and navigating UniProt databases. Curr. Protoc. Bioinformatics, 50, 1.27.1-1.27.10.
15. Fulton, D.L., Li, Y.Y., Laird, M.R., Horsman, B.G., Roche, F.M. and Brinkman, F.S. (2006) Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics, 7, 270.
16. Whiteside, M.D., Winsor, G.L., Laird, M.R. and Brinkman, F.S. (2013) OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acids Res., 41, D366-D376.
17. Galperin, M.Y., Makarova, K.S., Wolf, Y.I. and Koonin, E.V. (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res., 43, D261-D269.
18. Winsor, G.L., Van Rossum, T., Lo, R., Khaira, B., Whiteside, M.D., Hancock, R.E. and Brinkman, F.S. (2009) Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res., 37, D483-D488.
19. Ho Sui, S.J., Fedynak, A., Hsiao, W.W., Langille, M.G. and Brinkman, F.S. (2009) The association of virulence factors with genomic islands. PLoS One, 4, e8094.
20. NCBI Resource Coordinators. (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-D17.
21. Langille, M.G., Laird, M.R., Hsiao, W.W., Chiu, T.A., Eisen, J.A. and Brinkman, F.S. (2012) MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics, 28, 1947-1948.
22. Langille, M.G., Hsiao, W.W. and Brinkman, F.S. (2010) Detecting genomic islands using bioinformatics approaches. Nat. Rev. Microbiol., 8, 373-382.
23. Che, D., Hasan, M.S. and Chen, B. (2014) Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. Pathogens, 3, 36-56.
24. Dhillon, B.K., Laird, M.R., Shay, J.A., Winsor, G.L., Lo, R., Nizam, F., Pereira, S.K., Waglechner, N., McArthur, A.G., Langille, M.G. et al. (2015) Island Viewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res., 43, W104-W108.
25. Liu, B. and Pop, M. (2009) ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res., 37, D443-D447.
26. McArthur, A.G., Waglechner, N., Nizam, F., Yan, A., Azad, M.A., Baylay, A.J., Bhullar, K., Canova, M.J., De Pascale, G., Ejim, L. et al. (2013) The Comprehensive Antibiotic Resistance Database. Antimicrob. Agents Chemother., 57, 3348-3357.
27. Kingsford, C.L., Ayanbule, K. and Salzberg, S.L. (2007) Rapid, accurate, computational discovery of rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol., 8, R22.
28. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
29. Winkler, W.C., Cohen-Chalamish, S. and Breaker, R.R. (2002) An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U. S. A., 99, 15908-15913.
30. Bi, X. and Liu, L.F. (1996) DNA rearrangement mediated by inverted repeats. Proc. Natl. Acad. Sci. U. S. A., 93, 819-823.
31. Laird, M.R., Langille, M.G. and Brinkman, F.S. (2015) GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. Bioinformatics, 31, 3348-3349.
32. Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P. et al. (2015) STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
33. Grote, A., Klein, J., Retter, I., Haddad, I., Behling, S., Bunk, B., Biegler, I., Yarmolinetz, S., Jahn, D. and Munch, R. (2009) PRODORIC (release 2009): A database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res., 37, D61-D65.
34. Cipriano, M.J., Novichkov, P.N., Kazakov, A.E., Rodionov, D.A., Arkin, A.P., Gelfand, M.S. and Dubchak, I. (2013) RegTransBase-a database of regulatory sequences and interactions based on literature: A resource for investigating transcriptional regulation in prokaryotes. BMC Genomics, 14, 213.
35. Kilic, S., White, E.R., Sagitova, D.M., Cornish, J.P. and Erill, I. (2014) CollecTF: a database of experimentally validated transcription factor-binding sites in bacteria. Nucleic Acids Res., 42, D156-D160.
36. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
37. Stein, L.D. (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief. Bioinform., 14, 162-171.
38. Westesson, O., Skinner, M. and Holmes, I. (2013) Visualizing next-generation sequencing data with JBrowse. Brief. Bioinform., 14, 172-177.
39. Romero, P. and Karp, P. (2003) PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa. J. Mol. Microbiol. Biotechnol., 5, 230-239.
40. Tatusova, T., Ciufo, S., Federhen, S., Fedorov, B., McVeigh, R., O'Neill, K., Tolstoy, I. and Zaslavsky, L. (2015) Update on RefSeq microbial genomes resources. Nucleic Acids Res., 43, D599-D605.
41. Freschi, L., Jeukens, J., Kukavica-Ibrulj, I., Boyle, B., Dupont, M., Laroche, J., Larose, S., Maaroufi, H., Fothergill, J.L., Moore, M. et al. (2015) Clinical utilization of genomics data produced by the International Pseudomonas aeruginosa Consortium. Front. Microbiol., 6, 1036.
42. Markussen, T., Marvig, R.L., Gomez-Lozano, M., Aanaes, K., Burleigh, A.E., Hoiby, N., Johansen, H.K., Molin, S. and Jelsbak, L. (2014) Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa. MBio, 5, e01592-e01514.
43. Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J.R., Amaral-Zettler, L., Gilbert, J.A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G. et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol., 29, 415-420.
44. Reddy, T.B., Thomas, A.D., Stamatis, D., Bertsch, J., Isbandi, M., Jansson, J., Mallajosyula, J., Pagani, I., Lobos, E.A. and Kyrpides, N.C. (2015) The Genomes OnLine Database (GOLD) v.5: A metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res., 43, D1099-D1106.