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Using the National Microbial Pathogen Data Resource
Author(s) -
McNeil Leslie Klis,
Overbeek Ross,
Stevens Rick
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a863-c
Subject(s) - organism , computational biology , biology , genome , context (archaeology) , gene , encode , genetics , dna sequencing , cluster analysis , biodefense , dna microarray , computer science , microbiology and biotechnology , paleontology , gene expression , machine learning
The National Microbial Pathogen Data Resource ( www.nmpdr.org ) provides the advanced bioinformatics environment needed to identify genetic polymorphisms correlated with pathogenicity, drug resistance, morbidity, and infectivity. NMPDR contains the complete genomes of 29 strains of pathogenic bacteria that are the focus of our annotators, as well as the genomes of 347 other organisms that provide a broad context for comparative analysis across three Domains. Results of precomputed clustering analyses are retrieved in tabular or graphic format with one‐click tools. Preserved clustering on chromosomes of closely or distantly related organisms implies a functional association of the genes. Clustering analysis, combined with annotated functional subsystem information, can be used to identify genes that encode functions known to be present in an organism, but which are performed by divergent proteins not recognized by sequence similarity. Student and professional investigators can browse reactions and subsystems to develop accurate, detailed reconstructions of the metabolic networks of any sequenced organism. NMPDR data include DNA, RNA, and protein sequences, functional roles, evidence codes, subsystems, functional clusters, and microarray results. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms, for example, pathogenic and non‐pathogenic strains of Strep. NMPDR is funded by the NIAID to support research in biodefense and emerging or re‐emerging pathogens.