Chet RAYMO
A follow up for microbial databases
As novel sequencing techniques develops it becomes essential to construct databases with a large number of genomes. A collaboration with the Beijing Genome Institute located in Shenzhen, China, will provide novel information. It mirrored the GenoChore suite, before creating a novel suite on a completely novel data schema, until 2016. Unfortunately, because of changes at the head of the Chinese National DataBank at the BGI, this service was discontinued, and the address http://microme.genomics.org.cn/ is no longer valid.
When you use the databases please remember that the only way for us to provide continuous support is to show granting agencies that this work is used. Please quote the reference articles in your work.
The initial data model and algorithm is published in:
G Fang, C Ho, YW Qiu, V
Cubas, Z Yu, C Cabau, F Cheung, I Moszer, A Danchin
Specialized
microbial databases for inductive exploration of microbial
genome sequences
BMC Genomics (2005) 6: 14
For resequencing please quote:
V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, TZ Wang, I Moszer, C Médigue, A DanchinFor an update with the methionine salvage pathway
please quote:
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E Belda, A Sekowska, F Le Fèvre, A
Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A
Danchin An updated metabolic view of the Bacillus subtilis 168 genome Microbiology (2013) 159: 757-770. doi: 10.1099/mic.0.064691-0 |
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A Sekowska, H Ashida, A Danchin Revisiting the methionine salvage pathway and its paralogues Microb Biotechnol. (2019) 12: 77-97 doi: 10.1111/1751-7915.13324 |
For an update after 20 years please quote:
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R Borriss, A Danchin,
CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement Microb Biotechnol. (2018) 11: 3-17 doi: 10.1111/1751-7915.12461 |
Escherichia coli K12 (MG1655)
Colibri
Please quote:
C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654C. Médigue, T. Rouxel, P. Vigier, A. Hénaut & A. Danchin
Evidence for horizontal gene transfer in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856
Photorhabdus luminescens TT01
PhotoScope
Please quote:
E. Duchaud, C. Rusniok, L. Frangeul, C. Buchrieser, A. Givaudan, S. Taourit, S. Bocs, C. Boursaux-Eude, M. Chandler, J-F. Charles, E. Dassa, R. Derose, S. Derzelle, G. Freyssinet, S. Gaudriault, C. Médigue, A. Lanois, K. Powell, P. Siguier , R. Vincent, V. Wingate, M. Zouine, P. Glaser, N. Boemare, A. Danchin & F. Kunst
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.
Nature Biotechnol (2003) 21: 1307-1313
Staphylococcus epidermidis ATCC 12228 | ||
Y.Q. Zhang, S.X. Ren, H.L. Li, Y.X. Wang, G. Fu, J. Yang,
Z.Q. Qin, Y.G. Miao, W.Y. Wang, R.S. Chen, Y. Shen, Z. Chen,
Z.H. Yuan, G.P. Zhao, D. Qu, A. Danchin & Y.M. Wen Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol Microbiol (2003) 49:1577-1593 |
and the Beijing Genome Centre (China)
Thermoanaerobacter tencongensis | ||
and Fondaçao de Amparo a Pesquisa do Estado da Sao Paolo (Brasil)
Xylella fastidiosa | ||
and also, at the HKU Computer Centre
Clostridium acetobutylicum
Bacillus anthracis | ||
Bacillus cereus | ||
Campylobacter jejuni | ||
Haemophilus influenzae | ||
Neisseria meningitidis | ||
Pseudomonas aeruginosa | ||
Pseudomonas putida | ||
Vibrio cholerae | ||
Vibrio vulnificus | ||
Pseudoalteromonas haloplanktis TAC125 | ||
Please quote:
C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino, J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, G von Heijne, A Danchin
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Genome Res (2005) 15: 1325-1335
Encephalitozoon cuniculi | ||