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

By Geoffrey L. Winsor, David K. W. Lam, L. Fleming, Raymond Lo, M. D. Whiteside, N. Y. Yu, Robert E. W. Hancock, Fiona S. L. Brinkman. Nucleic Acids Res., 2010

669 citations recorded by the source corpus.

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. 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 for other genera-level research communities.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/90544ddab3befa67f45bea44b7b8be37179e0ae8

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Citations in the corpus

The GOA database: Gene Ontology annotation updates for 2015 (2014, methodology): “We incorporate annotations from 41 external groups and the level of contribution from each group can vary widely; since 2011 we have incorporated manual annotation datasets from the following groups: Aspergillus Genome Database (12), Pseudomonas Genome Database (13), the Community Assessment of Comm”
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012, methodology): “The Pseudomonas genome database [150] was consulted to obtain information on previouslypublished genomes for comparative purposes.”
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NCBI prokaryotic genome annotation pipeline (2016, methodology): “To further aims of generating consistent annotation, NCBI offers execution of the PGAP pipeline for all prokaryotic GenBank submissions, and it (36).”
Activities at the Universal Protein Resource (UniProt) (2013, background): “…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 Energy processes Gene Ontology Project (MENGO http://www.mengo.bioinformatics.vt.edu), from…”
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions (2016, methodology): “The DNA sequences of 13 strains that have been sequenced before were obtained from the Pseudomonas Genome Database (64).”
CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation (2014, methodology): “We also used the newly documented Gram-negative Pseudomonas aeruginosa PA01 genome/ proteome sequence dataset [31] (http://www.pseudomonas.com/), which contains, in part, hypothetical and uncharacterized proteins that can be difficult to functionally annotate because homologs or useful GO…”
RefSeq microbial genomes database: new representation and annotation strategy (2013, background): “MG165 (17), tuberculosis pathogens (18) and Pseudomonas strains (19).”