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Nucleic Acids Research Advance Access originally published online on December 1, 2006
Nucleic Acids Research 2007 35(Database issue):D347-D353; doi:10.1093/nar/gkl947
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Nucleic Acids Research, 2007, Vol. 35, Database issue D347-D353
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

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

Leslie Klis McNeil1,*, Claudia Reich1,2, Ramy K. Aziz3, Daniela Bartels4, Matthew Cohoon4, Terry Disz4, Robert A. Edwards5,6,7, Svetlana Gerdes5, Kaitlyn Hwang4,8, Michael Kubal4, Gohar Rem Margaryan4, Folker Meyer4,8, William Mihalo4, Gary J. Olsen2, Robert Olson4, Andrei Osterman5,7, Daniel Paarmann4, Tobias Paczian4, Bruce Parrello5, Gordon D. Pusch4,5, Dmitry A. Rodionov7, Xinghua Shi4, Olga Vassieva5,9, Veronika Vonstein5, Olga Zagnitko5, Fangfang Xia4, Jenifer Zinner4, Ross Overbeek5 and Rick Stevens4,8

1 National Center for Supercomputing Applications Urbana, IL 61801, USA 2 Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL 61801, USA 3 Department of Microbiology and Immunology, College of Pharmacy, Cairo University Cairo, Egypt 4 Computation Institute, University of Chicago Chicago, IL 60637, USA 5 Fellowship for Interpretation of Genomes, Burr Ridge IL 60527, USA 6 San Diego State University, San Diego CA 92182, USA 7 The Burnham Institute, San Diego CA 92037, USA 8 Mathematics and Computer Science Division, Argonne National Laboratory Argonne, IL 60439, USA 9 Biomedical Research Centre, University of Dundee Dundee DD14HN UK

*To whom correspondence should be addressed. Tel: +1 217 244 0597; Fax: +1 217 244 2909; Email: lkmcneil{at}ncsa.uiuc.edu

Received August 15, 2006. Revised September 21, 2006. Accepted October 20, 2006.

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 ~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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