The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
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.
McNeil
Leslie Klis
LK
National Center for Supercomputing Applications, Urbana, IL 61801, USA. lkmcneil@ncsa.uiuc.edu
Reich
Claudia
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Aziz
Ramy K
RK
Bartels
Daniela
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Cohoon
Matthew
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Disz
Terry
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Edwards
Robert A
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Gerdes
Svetlana
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Hwang
Kaitlyn
K
Kubal
Michael
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Margaryan
Gohar Rem
GR
Meyer
Folker
F
Mihalo
William
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Olsen
Gary J
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Olson
Robert
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Osterman
Andrei
A
Paarmann
Daniel
D
Paczian
Tobias
T
Parrello
Bruce
B
Pusch
Gordon D
GD
Rodionov
Dmitry A
DA
Shi
Xinghua
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Vassieva
Olga
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Vonstein
Veronika
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Zagnitko
Olga
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Xia
Fangfang
F
Zinner
Jenifer
J
Overbeek
Ross
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Stevens
Rick
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D001419:Bacteria / Q000187:drug effects / Q000378:metabolism / Q000472:pathogenicity; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology; D004269:DNA, Bacterial / Q000737:chemistry; D030561:Databases, Nucleic Acid; D016503:Drug Delivery Systems; D005798:Genes, Bacterial; D020043:Genes, Essential; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
D001426:Bacterial Proteins; D004269:DNA, Bacterial