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The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
The National Microbial Pathogen Data Resource (NMPDR) () 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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751540/ https://www.ncbi.nlm.nih.gov/pubmed/17145713 http://dx.doi.org/10.1093/nar/gkl947 |
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author | 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 |
author_facet | 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 |
author_sort | McNeil, Leslie Klis |
collection | PubMed |
description | The National Microbial Pathogen Data Resource (NMPDR) () 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. |
format | Text |
id | pubmed-1751540 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-17515402007-02-22 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 Nucleic Acids Res Articles The National Microbial Pathogen Data Resource (NMPDR) () 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. Oxford University Press 2007-01 2006-12-01 /pmc/articles/PMC1751540/ /pubmed/17145713 http://dx.doi.org/10.1093/nar/gkl947 Text en © 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. |
spellingShingle | Articles 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 The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title | The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title_full | The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title_fullStr | The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title_full_unstemmed | The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title_short | The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation |
title_sort | national microbial pathogen database resource (nmpdr): a genomics platform based on subsystem annotation |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751540/ https://www.ncbi.nlm.nih.gov/pubmed/17145713 http://dx.doi.org/10.1093/nar/gkl947 |
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