Nucleic Acids Research Advance Access originally published online on October 31, 2008
Nucleic Acids Research 2009 37(Database issue):D483-D488; doi:10.1093/nar/gkn861
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, Database issue D483-D488
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 and 2Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
*To whom correspondence should be addressed. Tel: +1 778 782 5646; Fax: +1 778 782 5583; Email: brinkman{at}sfu.ca
Received September 16, 2008. Revised October 15, 2008. Accepted October 16, 2008.
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. Barraud, D. Schleheck, J. Klebensberger, J. S. Webb, D. J. Hassett, S. A. Rice, and S. Kjelleberg Nitric Oxide Signaling in Pseudomonas aeruginosa Biofilms Mediates Phosphodiesterase Activity, Decreased Cyclic Di-GMP Levels, and Enhanced Dispersal J. Bacteriol., December 1, 2009; 191(23): 7333 - 7342. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. M. Markowitz, K. Mavromatis, N. N. Ivanova, I-M. A. Chen, K. Chu, and N. C. Kyrpides IMG ER: a system for microbial genome annotation expert review and curation Bioinformatics, September 1, 2009; 25(17): 2271 - 2278. [Abstract] [Full Text] [PDF]
|
|