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 ∼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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | D347-D353 |
| Journal | Nucleic acids research |
| Volume | 35 |
| Issue number | SUPPL. 1 |
| DOIs | |
| State | Published - Jan 1 2007 |
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ASJC Scopus subject areas
- Genetics
Cite this
The National Microbial Pathogen Database Resource (NMPDR) : A genomics platform based on subsystem annotation. / McNeil, Leslie Klis; Reich, Claudia; Aziz, Ramy K.; Bartels, Daniela; Cohoon, Matthew; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Hwang, Kaitlyn; Kubal, Michael; Margaryan, Gohar Rem; Meyer, Folker; Mihalo, William; Olsen, Gary J.; Olson, Robert; Osterman, Andrei; Paarmann, Daniel; Paczian, Tobias; Parrello, Bruce; Pusch, Gordon D.; Rodionov, Dmitry A.; Shi, Xinghua; Vassieva, Olga; Vonstein, Veronika; Zagnitko, Olga; Xia, Fangfang; Zinner, Jenifer; Overbeek, Ross; Stevens, Rick.
In: Nucleic acids research, Vol. 35, No. SUPPL. 1, 01.01.2007, p. D347-D353.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - The National Microbial Pathogen Database Resource (NMPDR)
T2 - A genomics platform based on subsystem annotation
AU - McNeil, Leslie Klis
AU - Reich, Claudia
AU - Aziz, Ramy K.
AU - Bartels, Daniela
AU - Cohoon, Matthew
AU - Disz, Terry
AU - Edwards, Robert A.
AU - Gerdes, Svetlana
AU - Hwang, Kaitlyn
AU - Kubal, Michael
AU - Margaryan, Gohar Rem
AU - Meyer, Folker
AU - Mihalo, William
AU - Olsen, Gary J.
AU - Olson, Robert
AU - Osterman, Andrei
AU - Paarmann, Daniel
AU - Paczian, Tobias
AU - Parrello, Bruce
AU - Pusch, Gordon D.
AU - Rodionov, Dmitry A.
AU - Shi, Xinghua
AU - Vassieva, Olga
AU - Vonstein, Veronika
AU - Zagnitko, Olga
AU - Xia, Fangfang
AU - Zinner, Jenifer
AU - Overbeek, Ross
AU - Stevens, Rick
PY - 2007/1/1
Y1 - 2007/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33846119130&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33846119130&partnerID=8YFLogxK
U2 - 10.1093/nar/gkl947
DO - 10.1093/nar/gkl947
M3 - Article
C2 - 17145713
AN - SCOPUS:33846119130
VL - 35
SP - D347-D353
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - SUPPL. 1
ER -