The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
Open accessAbstract
Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license.
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Cites
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,641
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Multiple sequence alignment with the Clustal series of programs
Chenna, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg500 · Cited by 4,875
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S. L., Hufnagle, W. O., Kowalik, D. J., Lagrou, M., et al. (2000) · Nature · doi:10.1038/35023079 · Cited by 4,573
Self-citationThe COG database: a tool for genome-scale analysis of protein functions and evolution
Tatusov, R. L. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.33 · Cited by 4,520
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,430
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., et al. (2002) · Genome Research · doi:10.1101/gr.403602 · Cited by 1,145
Comprehensive transposon mutant library of Pseudomonas aeruginosa
Jacobs, M. A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., Will, O., Kaul, R., Raymond, C., Levy, R., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2036282100 · Cited by 1,126
An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
Liberati, N. T., Urbach, J. M., Miyata, S., Lee, D. G., Drenkard, E., Wu, G., Villanueva, J., Wei, T., & Ausubel, F. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511100103 · Cited by 968
Cited by
Winsor, G. L., Griffiths, E. J., Lo, R., Dhillon, B. K., Shay, J. A., & Brinkman, F. S. L. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1227 · Cited by 1,050
Self-citationPseudomonas genomes: diverse and adaptable
Silby, M. W., Winstanley, C., Godfrey, S. A. C., Levy, S. B., & Jackson, R. W. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00269.x · Cited by 960
IMG ER: a system for microbial genome annotation expert review and curation
Markowitz, V. M., Mavromatis, K., Ivanova, N. N., Chen, I.-M. A., Chu, K., & Kyrpides, N. C. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp393 · Cited by 817
Pseudomonas biofilm matrix composition and niche biology
Mann, E. E., & Wozniak, D. J. (2012) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00322.x · Cited by 606
Barraud, N., Schleheck, D., Klebensberger, J., Webb, J. S., Hassett, D. J., Rice, S. A., & Kjelleberg, S. (2009) · Journal of Bacteriology · doi:10.1128/jb.00975-09 · Cited by 513
Metadata
- Authors
- Winsor, G. L., Van Rossum, T., Lo, R., Khaira, B., Whiteside, M. D., Hancock, R. E. W., & Brinkman, F. S. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-01
- Volume
- 37
- Issue
- Database
- Pages
- D483-D488
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2155954664
- Cited by
- 256
- References
- 33
- FWCI
- 12.90
- Type
- journal article
- Language
- en
- Open access
- gold
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- Winsor, G. L., Van Rossum, T., Lo, R., Khaira, B., Whiteside, M. D., Hancock, R. E. W., & Brinkman, F. S. L. (2009). Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Research. https://doi.org/10.1093/nar/gkn861
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