Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan;38(Database issue):D408-14.
doi: 10.1093/nar/gkp850. Epub 2009 Oct 20.

Pathema: A Clade-Specific Bioinformatics Resource Center for Pathogen Research

Free PMC article

Pathema: A Clade-Specific Bioinformatics Resource Center for Pathogen Research

Lauren M Brinkac et al. Nucleic Acids Res. .
Free PMC article


Pathema ( is one of the eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infectious Disease (NIAID) designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms.


Figure 1.
Figure 1.
Pathema-Burkholderia Comparative Tools. This figure shows some of the comparative tools available on Pathema for the Burkholderia clade. (A) Protein orthologous cluster: Burkholderia multidrug efflux pump AmrA region and Clustal alignments; (B) Comparative genomic region: Burkholderia whole genomes aligned to a reference; (C) Evidence comparison: differences in evidence occurrence across multiple Burkholderia genomes and phylogeny of selected proteins.

Similar articles

See all similar articles

Cited by 14 articles

See all "Cited by" articles


    1. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect. Immun. 2007;75:3212–3219. - PMC - PubMed
    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2008;36:D25–D30. - PMC - PubMed
    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. - PMC - PubMed
    1. Darling RG, Catlett CL, Huebner KD, Jarrett DG. Threats in bioterrorism. I: CDC category A agents. Emerg. Med. Clin. North Am. 2002;20:273–309. - PubMed
    1. Moran GJ. Threats in bioterrorism. II: CDC category B and C agents. Emerg. Med. Clin. North Am. 2002;20:311–330. - PubMed

Publication types