TY - JOUR
T1 - Pseudomonas Genome Database
T2 - Facilitating user-friendly, comprehensive comparisons of microbial genomes
AU - Winsor, Geoffrey L.
AU - Van Rossum, Thea
AU - Lo, Raymond
AU - Khaira, Bhavjinder
AU - Whiteside, Matthew D.
AU - Hancock, Robert E.W.
AU - Brinkman, Fiona S.L.
N1 - Funding Information:
This work was supported by the Cystic Fibrosis Foundation. M.D.W. holds a Junior Graduate Studentship Award from the Michael Smith Foundation for Health Research (MSFHR). F.S.L.B. is a MSFHR. Senior Scholar and Canadian Institutes for Health Research New Investigator. R.E.W.H. holds a Canada Research Chair. Funding for open access charge: Cystic Fibrosis Foundation and SFU Community Trust Endowment Fund.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=58149197594&partnerID=8YFLogxK
U2 - 10.1093/nar/gkn861
DO - 10.1093/nar/gkn861
M3 - Article
C2 - 18978025
AN - SCOPUS:58149197594
SN - 0305-1048
VL - 37
SP - D483-D488
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -