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Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation

G. L. Winsor
2004 Nucleic Acids Research  
Using the Pseudomonas aeruginosa Genome Project as a test case, we have developed a database and submission system to facilitate a community-based approach to continually updated genome annotation (http  ...  be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach.  ...  Ancillary funding provided by Genome Prairie, Genome BC, Inimex Pharmaceuticals and the CCFF.  ... 
doi:10.1093/nar/gki047 pmid:15608211 pmcid:PMC540001 fatcat:zjpa3l66nre73fr4z3vtfwycsm

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

G. L. Winsor, D. K. W. Lam, L. Fleming, R. Lo, M. D. Whiteside, N. Y. Yu, R. E. W. Hancock, F. S. L. Brinkman
2010 Nucleic Acids Research  
The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented  ...  and manually curated annotation updates.  ...  We also thank all 150 community annotation update participants (listed at http://www .pseudomonas.com/researchList.jsp) for their valuable contributions and all the Pseudomonas genome projects, without  ... 
doi:10.1093/nar/gkq869 pmid:20929876 pmcid:PMC3013766 fatcat:filomrmiwzha5fyhyounmec5l4

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

G. L. Winsor, T. Van Rossum, R. Lo, B. Khaira, M. D. Whiteside, R. E. W. Hancock, F. S. L. Brinkman
2009 Nucleic Acids Research  
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  ...  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.  ...  ACKNOWLEDGEMENTS We thank all the Pseudomonas genome projects, without which this database would not be possible.  ... 
doi:10.1093/nar/gkn861 pmid:18978025 pmcid:PMC2686508 fatcat:lrrl3xj23zhqbpreq33yqjlq5u

Enhanced annotations and features for comparing thousands ofPseudomonasgenomes in the Pseudomonas genome database

Geoffrey L. Winsor, Emma J. Griffiths, Raymond Lo, Bhavjinder K. Dhillon, Julie A. Shay, Fiona S. L. Brinkman
2015 Nucleic Acids Research  
The Pseudomonas Genome Database (http://www. pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome  ...  We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas  ...  Hancock for valuable feedback that helped us improve the website functionality and the contributions of the Pseudomonas research community in assisting with annotation updates.  ... 
doi:10.1093/nar/gkv1227 pmid:26578582 pmcid:PMC4702867 fatcat:uouhzmq4brbwrmbb5deiao4qfy

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database

Weiliang Huang, Luke K Brewer, Jace W Jones, Angela T Nguyen, Ana Marcu, David S Wishart, Amanda G Oglesby-Sherrouse, Maureen A Kane, Angela Wilks
2017 Nucleic Acids Research  
The Pseudomonas aeruginosa Metabolome Database (PAMDB, http://pseudomonas.umaryland. edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa.  ...  The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories.  ...  Extensive P. aeruginosa gene and protein data is available in several excellent resources including the Pseudomonas Genome Database that evolved from the Pseudomonas Community Annotation Project (PseudoCAP  ... 
doi:10.1093/nar/gkx1061 pmid:29106626 pmcid:PMC5753269 fatcat:6wa4oukjrfeg7eyvuirbobefna

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

M. A. Oberhardt, J. Puchalka, K. E. Fryer, V. A. P. Martins dos Santos, J. A. Papin
2008 Journal of Bacteriology  
To this end, we reconstructed a genome-scale metabolic network of Pseudomonas aeruginosa PAO1. This reconstruction accounts for 1056 genes (19% of the genome), 1030 proteins, and 883 reactions.  ...  Pseudomonas aeruginosa is a major life-threatening opportunistic pathogen that commonly infects immunocompromised patients.  ...  Timmis, Arvind Chavali, Erwin Gianchandani, Corinne Locke, and Rhiannon Franck for their thoughtful comments and contributions to this study.  ... 
doi:10.1128/jb.01583-07 pmid:18192387 pmcid:PMC2293256 fatcat:jh2k6olaynfllkkpzihxgo7pt4

Sequencing of the Pseudomonas aeruginosa and Burkholderia cepacia genomes and their applications in relation to cystic fibrosis

Deborah A Miller, Eshwar Mahenthiralingam
2003 Journal of the Royal Society of Medicine  
and annotation of this genome sequence was aided by the expertise of scientists in this field and initiated the formation of a group of volunteers called the Pseudomonas aeruginosa Community Annotation  ...  The work of this group still continues; as hypothetical genes are determined, the sequence and annotation is updated to include this information.  ... 
pmid:12906327 pmcid:PMC1308789 fatcat:fdusumbbaffxnh2gezzg4gr2ny

Microbial genome data resources

Victor M Markowitz
2007 Current Opinion in Biotechnology  
Peer review annotation mechanisms have been employed primarily for specific organisms, such as Pseudomonas syringae pv. tomato [25] and Pseudomonas aeruginosa pv. [26] .  ...  The latter is especially important given the inherent complexity of resolving gene model and annotation differences or inconsistencies in the context of continuously changing annotation methods and evolving  ... 
doi:10.1016/j.copbio.2007.04.005 pmid:17467973 fatcat:xar5m3dtf5dmtglad2pe6l2nku

Activities at the Universal Protein Resource (UniProt)

2013 Nucleic Acids Research  
These annotations are to proteins from Aspergillus by the AspGD project (6), from the Pseudomonas aeruginosa Community Annotation Project (PseudoCAP) (9) , from archaeal and bacterial species by the Microbial  ...  ; the UniProt Reference Clusters (UniRef) (2) , which merge closely related sequences based on sequence identity to facilitate sequence similarity searches; and the UniProt Metagenomic and Environmental  ... 
doi:10.1093/nar/gkt1140 pmid:24253303 pmcid:PMC3965022 fatcat:ymvqbpyhizafba7upcn222a6ty

MicroScope: a platform for microbial genome annotation and comparative genomics

D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, C. Médigue
2009 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors would like to thank all MaGe users for their feedback that helped greatly in optimizing and improving many functionalities of the system.  ...  steps: first, an update of the reference genome annotation, and second, the annotation of the new genomes based on the re-annotated one.  ...  - Chromosomal location of genes participating in the degradation of purines in Pseudomonas aeruginosa.  ... 
doi:10.1093/database/bap021 pmid:20157493 pmcid:PMC2790312 fatcat:3n3cu7s5mvazzk5n4go46hsipi

Lineage-specific regions inPseudomonas syringaepv tomato DC3000

VINITA JOARDAR, MAGDALEN LINDEBERG, DAVID J. SCHNEIDER, ALAN COLLMER, C. ROBIN BUELL
2005 Molecular plant pathology  
Deboy (Microbial Genomics) and Samuel V. Angiuoli (Bioinformatics) at The Institute for Genomic Research for their contribution to the work.  ...  The PAO1 genome has been annotated by the P. aeruginosa community and can be obtained from PseudoCAP (http://www.pseudomonas.com).  ...  The PAO1 data used represent the 8 October 2003 version of the continually updated, reviewed, P. aeruginosa PAO1 genome annotation from PseudoCAP (http://www.pseudomonas.com).  ... 
doi:10.1111/j.1364-3703.2004.00263.x pmid:20565638 fatcat:lakacdbngjd4zo24kpwibnq6ta

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

2017 Briefings in Bioinformatics  
In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data.  ...  The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative  ...  Acknowledgements The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
doi:10.1093/bib/bbx113 pmid:28968784 pmcid:PMC6931091 fatcat:3kbei6onubhe3cobdiuk72xt4a

The analysis of the role of MexAB-OprM on quorum sensing homeostasis shows that the apparent redundancy of Pseudomonas aeruginosa multidrug efflux pumps allows keeping the robustness and the plasticity of this intercellular signaling network [article]

Manuel Alcalde-Rico, Jorge Olivares-Pacheco, Nigel M Halliday, Miguel Cámara, José Luis Martínez
2020 bioRxiv   pre-print
In the case of Pseudomonas aeruginosa, it has been stated that overexpression of different efflux pumps is linked to the impairment of the quorum sensing (QS) response.  ...  In addition to their role in resistance to antimicrobials, efflux pumps are ancient and conserved elements with relevant roles in different aspects of the bacterial physiology.  ...  of Pseudomonas genomes in the Pseudomonas genome database. 632 Nucleic Acids Res, 2016. 44(D1): p.  ... 
doi:10.1101/2020.03.10.986737 fatcat:s4ujmxuwcreivp67vqt2f3fbcq

Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens

Mustafa Sertbas, Kutlu O. Ulgen
2020 Frontiers in Cell and Developmental Biology  
Genome-scale metabolic modeling is ever increasingly used tool for biomedical applications including the elucidation of antibiotic resistance, virulence, single pathogen mechanisms and pathogen-host interaction  ...  Here, we reviewed the current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies  ...  Together with other biochemical databases, Pseudomonas aeruginosa specific database PseudoCAP provides valuable metabolic information for GEM reconstruction of this organism (Winsor et al., 2005) .  ... 
doi:10.3389/fcell.2020.566702 pmid:33251208 pmcid:PMC7673413 fatcat:bzxpxhdfibe5voxtahevqniqi4

Functional annotation of Pseudomonas aeruginosa membrane proteins in response to micronutrients

Bradley W. Wright
2022
The opportunistic pathogen Pseudomonas aeruginosa PAO1 is well known for its environmental and metabolic versatility, and large genome of 6.3Mbp.  ...  Studying the proteome is key to providing accurate, and informative genome annotation.  ...  PGD was developed originally to facilitate continually updated community based genome annotation (38) for P. aeruginosa but in the years subsequent to the PAO1 genome release there has been much work  ... 
doi:10.25949/19432058.v1 fatcat:cjm2cwigwvd2vden3wjxffy5uu
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