Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.
Geoffrey L. Winsor,Raymond Lo,Shannan J. Ho Sui,Korine S.E. Ung,Shaoshan Huang,Dean Cheng,Wai Kay Ho Ching,Robert E. W. Hancock,Fiona S. L. Brinkman +8 more
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TLDR
This database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach.Abstract:
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://www.pseudomonas.com). Researchers submit proposed annotation updates through one of three web-based form options which are then subjected to review, and if accepted, entered into both the database and log file of updates with author acknowledgement. In addition, a coordinator continually reviews literature for suitable updates, as we have found such reviews to be the most efficient. Both the annotations database and updates-log database have Boolean search capability with the ability to sort results and download all data or search results as tab-delimited files. To complement this peer-reviewed genome annotation, we also provide a linked GBrowse view which displays alternate annotations. Additional tools and analyses are also integrated, including PseudoCyc, and knockout mutant information. We propose that this database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach. The source code is freely available under GNU General Public Licence.read more
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Pseudomonas aeruginosa : new insights into pathogenesis and host defenses
TL;DR: An overview of the host response and how the genomic capacity of P. aeruginosa contributes to the pathogenesis and persistence of these infections is provided.
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Aminoglycoside Modifying Enzymes
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Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
Geoffrey L. Winsor,David Lam,Leanne Fleming,Raymond Lo,Matthew D. Whiteside,Nancy Yiu-Lin Yu,Robert E. W. Hancock,Fiona S. L. Brinkman +7 more
TL;DR: The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences, which aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies.
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