Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jan 4;44(D1):D646-53.
doi: 10.1093/nar/gkv1227. Epub 2015 Nov 17.

Enhanced Annotations and Features for Comparing Thousands of Pseudomonas Genomes in the Pseudomonas Genome Database

Affiliations
Free PMC article

Enhanced Annotations and Features for Comparing Thousands of Pseudomonas Genomes in the Pseudomonas Genome Database

Geoffrey L Winsor et al. Nucleic Acids Res. .
Free PMC article

Abstract

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 annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. 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 community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches.

Figures

Figure 1.
Figure 1.
A representative view of the enhanced display of genome-wide data tailored to specific annotation types. In this example, Gene Ontology (GO) term annotations for Pseudomonas aeruginosa PAO1 can be customized to provide distinct subsets of data based on specific GO terms or types of evidence (e.g. based on GO or ECO evidence codes). Results can be downloaded in GO Annotation File 2.0 format suitable for downstream applications including differential expression analysis.
Figure 2.
Figure 2.
A wide range of genomic features are available for visualization through the Pseudomonas Genome Database implantation of GMOD's JBrowse viewer. This example shows an upper track containing glyphs corresponding to annotated Pseudomonas aeruginosa PAO1 genes, a middle XY-plot track representing RNA-Seq coverage based on an indexed bam file, and a lower track containing alignments of individual reads from the same file. Users can also open and view their own RNA-Seq data, variant files and GFF3 annotations in context of other up-to-date genomic features publicly available through the site. All data available through the interface can be further customized in the browser or downloaded in a range of different formats.

Similar articles

See all similar articles

Cited by 204 articles

See all "Cited by" articles

References

    1. Mathee K., Narasimhan G., Valdes C., Qiu X., Matewish J.M., Koehrsen M., Rokas A., Yandava C.N., Engels R., Zeng E., et al. Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. U. S. A. 2008;105:3100–3105. - PMC - PubMed
    1. Klockgether J., Cramer N., Wiehlmann L., Davenport C.F., Tummler B. Pseudomonas aeruginosa genomic structure and diversity. Front. Microbiol. 2011;2:150. - PMC - PubMed
    1. Winsor G.L., Lam D.K., Fleming L., Lo R., Whiteside M.D., Yu N.Y., Hancock R.E., Brinkman F.S. Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res. 2011;39:D596–D600. - PMC - PubMed
    1. Stover C.K., Pham X.Q., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., Brinkman F.S., Hufnagle W.O., Kowalik D.J., Lagrou M., et al. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature. 2000;406:959–964. - PubMed
    1. Brinkman F.S., Hancock R.E., Stover C.K. Sequencing solution: use volunteer annotators organized via internet. Nature. 2000;406:933. - PubMed

Publication types

Feedback