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Nucleic Acids Research Advance Access published online on October 20, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp850
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Pathema: a clade-specific bioinformatics resource center for pathogen research

Lauren M. Brinkac1, Tanja Davidsen1, Erin Beck1, Anuradha Ganapathy4, Elisabet Caler1, Robert J. Dodson1,2, A. Scott Durkin1, Derek M. Harkins1, Hernan Lorenzi1, Ramana Madupu1, Yinong Sebastian1,3, Susmita Shrivastava1, Mathangi Thiagarajan1, Joshua Orvis4, Jaideep P. Sundaram1, Jonathon Crabtree4, Kevin Galens4, Yongmei Zhao4,5, Jason M. Inman1, Robert Montgomery1, Seth Schobel1, Kevin Galinsky1, David M. Tanenbaum1, Adam Resnick1, Nikhat Zafar1, Owen White4 and Granger Sutton1,*

1J. Craig Venter Institute, Rockville, MD 20850, 2Northwestern University, Chicago, IL 60208, 3National Institutes of Health-NIAID, Bethesda, MD 20892, 4Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 and 5SAIC/National Cancer Institute, Gaithersburg, MD 20877, USA

*To whom correspondence should be addressed. Tel: +1 301 795 7293; Fax: +1 301 294 3142; Email: gsutton{at}jcvi.org

Received August 14, 2009. Revised September 17, 2009. Accepted September 18, 2009.

Pathema (http://pathema.jcvi.org) 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.


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