Pathema
Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services. Pathema was funded for five years from 2004 through a contract to The J. Craig Venter Institute, and is currently led by PI Granger Sutton. Pathema is the web resource for JCVI's NIAID-funded Bioinformatics Resource Center, and was one of eight such centers designed to support bio-defense and infectious disease research. The overarching  goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens ("Bacillus anthracis", "Clostridium botulinum", "Burkholderia mallei", "Burkholderia pseudomallei", "Clostridium perfringens", and "Entamoeba histolytica") involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics. Note to All Pathema Users. The Pathema BRC contract ended December 2009. At that time JCVI  ceased maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania supports all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. Please feel free to contact us if you have any questions about this transition. Pathema Analysis Tools. Pathema supports a suite of over 50 web-based single gene, whole-genome and multi-genome comparative  tools to facilitate analyses of genomic sequence and annotation data of over 80 NIAID Category A-C prokaryotic pathogens. Tools available on the BRC resource are developed and customized to best meet the scientific needs of the pathogen research community based on feedback solicited through community outreach. Additionally, they are designed to facilitate scientific exploration in the areas of functional curation, pathogenicity, therapeutics, comparative analysis and functional genomics. While every tool has several applications, taken together they provides numerous opportunities for discovery and hypothesis generation. The suite of Pathema analysis tools include: