The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation - PubMed (original) (raw)

. 2007 Jan;35(Database issue):D347-53.

doi: 10.1093/nar/gkl947. Epub 2006 Dec 1.

Claudia Reich, Ramy K Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Dmitry A Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross Overbeek, Rick Stevens

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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

Leslie Klis McNeil et al. Nucleic Acids Res. 2007 Jan.

Abstract

The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development.

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Figures

Figure 1

Figure 1

Compare regions shows a graphical display of homologous chromosomal regions that opens showing the five genomes with the highest score, based on similar proteins in this region, and phylogenetic distance. The display is centered on this focus PEG, which is shown in red and numbered 1. Sets of homologous genes share a color and a numerical label, which are ordered by frequency of co-localization with the focus PEG. The size of the region and the number of genomes may be reset. Clicking on any arrow in the display will refocus the comparison on that gene. The focus PEG always points to the right, even if it is located on the minus strand. The next and previous links allow you to walk the contig. This example shows a large, gray, pathogenecity island annotated in one strain of L.monocytogenes at the top, while at the bottom, Clostridium tetani shares only a homologous cytolysin with the Listeria. The gray proteins in the region of the C.tetani cytolysin are not homologous with the listerial proteins. The Listeria strain that seems to be lacking proteins represents the full length of a very short contig.

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