MicroScope: A platform for microbial genome annotation and comparative genomics

Database

Volumn 2009, Issue , 2009, Pages

  Vallenet, D ^a   Engelen, S ^a   Mornico, D ^a   Cruveiller, S ^a   Fleury, L ^a   Lajus, A ^a   Rouy, Z ^a   Roche, D ^a   Salvignol, G ^a   Scarpelli, C ^a   Medigue C ^a  

^a DIF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84908096911     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bap021     Document Type: Article

References (47)

1. Salzberg, S.L. (2007) Genome re-annotation: a wiki solution? Genome Biol., 8, 102.
2. Lima, T., Auchincloss, A.H., Coudert, E. et al. (2009) HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res., 37, D471-D478.
3. Klimke, W., Agarwala, R., Badretdin, A. et al. (2009) The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res., 37, D216-D223.
4. Overbeek, R., Begley, T., Butler, R.M. et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res., 33, 5691-5702.
5. Markowitz, V.M., Szeto, E., Palaniappan, K. et al. (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res., 36, D528-D533.
6. D'Ascenzo, M.D., Collmer, A. and Martin, G.B. (2004) PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucleic Acids Res., 32, 3124-3135.
7. Winsor, G.L., Lo, R., Sui, S.J. et al. (2005) Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res., 33, D338-D343.
8. Glasner, J.D., Rusch, M., Liss, P. et al. (2006) ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res., 34, D41-D45.
9. Hubbard, T.J., Aken, B.L., Ayling, S. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
10. Overbeek, R., Larsen, N., Walunas, T. et al. (2003) The ERGO genome analysis and discovery system. Nucleic Acids Res., 31, 164-171.
11. Walter, M.C., Rattei, T., Arnold, R. et al. (2009) PEDANT covers all complete RefSeq genomes. Nucleic Acids Res., 37, D408-D411.
12. Meyer, F., Goesmann, A., McHardy, A.C. et al. (2003) GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res., 31, 2187-2195.
13. Almeida, L.G., Paixao, R., Souza, R.C. et al. (2004) A system for automated bacterial (genome) integrated annotation - SABIA. Bioinformatics, 20, 2832-2833.
14. Bryson, K., Loux, V., Bossy, R. et al. (2006) AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res., 34, 3533-3545.
15. Pellegrini, M., Marcotte, E.M., Thompson, M.J. et al. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
16. Overbeek, R., Fonstein, M., D'Souza, M. et al. (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol., 1, 93-108.
17. Marcotte, E.M., Pellegrini, M., Ng, H.L. et al. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
18. Markowitz, V.M., Mavromatis, K., Ivanova, N.N. et al. (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics, 25, 2271-2278.
19. Vallenet, D., Labarre, L., Rouy, Z. et al. (2006) MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res., 34, 53-65.
20. Barbe, V., Vallenet, D., Fonknechten, N. et al. (2004) Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res., 32, 5766-5779.
21. Bairoch, A., Bougueleret, L., Altairac, S. et al. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
22. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
23. Bairoch, A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
24. Bocs, S., Cruveiller, S., Vallenet, D. et al. (2003) AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res., 31, 3723-3726.
25. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
26. Lagesen, K., Hallin, P., Rodland, E.A. et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res., 35, 3100-3108.
27. Gardner, P.P., Daub, J., Tate, J.G. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
28. Cruveiller, S., Le Saux, J., Vallenet, D. et al. (2005) MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. Nucleic Acids Res., 33, W471-W479.
29. Tatusov, R.L., Fedorova, N.D., Jackson, J.D. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
30. Hunter, S., Apweiler, R., Attwood, T.K. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
31. Claudel-Renard, C., Chevalet, C., Faraut, T. et al. (2003) Enzymespecific profiles for genome annotation: PRIAM. Nucleic Acids Res., 31, 6633-6639.
32. Sonnhammer, E.L., von Heijne, G. and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
33. Bendtsen, J.D., Nielsen, H., von Heijne, G. et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
34. Gardy, J.L., Laird, M.R., Chen, F. et al. (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics, 21, 617-623.
35. Karp, P.D., Paley, S. and Romero, P. (2002) The Pathway Tools software. Bioinformatics, 18 (Suppl. 1), S225-S232.
36. Waterhouse, A.M., Procter, J.B., Martin, D.M. et al. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
37. Kanehisa, M., Araki, M., Goto, S. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res, 36, D480-D484.
38. Hacker, J. and Carniel, E. (2001) Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep., 2, 376-381.
39. Caspi, R., Foerster, H., Fulcher, C.A. et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 36, D623-D631.
40. Serres, M.H. and Riley, M. (2000) MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics, 5, 205-222.
41. Selengut, J.D., Haft, D.H., Davidsen, T. et al. (2007) TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res., 35, D260-D264.
42. Gil, R., Silva, F.J., Pereto, J. et al. (2004) Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev., 68, 518-537.
43. Carver, T., Berriman, M., Tivey, A. et al. (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics, 24, 2672-2676.
44. Sayers, E.W., Barrett, T., Benson, D.A. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
45. Matsumoto, H., Ohta, S., Kobayashi, R. et al. (1978) Chromosomal location of genes participating in the degradation of purines in Pseudomonas aeruginosa. Mol. Gen. Genet., 167, 165-176.
46. Pelletier, E., Kreimeyer, A., Bocs, S. et al. (2008) 'Candidatus Cloacamonas acidaminovorans': genome sequence reconstruction provides a first glimpse of a new bacterial division. J. Bacteriol., 190, 2572-2579.
47. Saier, M.H. Jr., Tran, C.V. and Barabote, R.D. (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res., 34, D181-D186.