Pathema: A Bioinformatics Resource Center


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Conference: Functional Genomes of Microorganisms Conference, April 8-11, 2008 in Paris, France.
Presenter: Lauren Brinkac

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Pathema: A Bioinformatics Resource Center

  1. 1. PATHEMA: A BIOINFORMATICS RESOURCE CENTER Lauren Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy*, Jay Sundaram, Scott Durkin, Owen White*, Granger Sutton J. Craig Venter Institute, 9704 Medical Center Dr. Rockville, MD, 20850 USA * Institute for Genome Sciences, 685 West Baltimore St., Baltimore, MD, 21201 USA Abstract Pathema Organisms Available Genomes Genome Graphical Pathema ( is a NIAID Bioinformatics Resource Center Displays designed to support bio-defense and infectious disease research. Pathema Current # Current # Future Total provides detailed curation of six target pathogens: Bacillus anthracis, Clostridium Genus Species Strains Genomes Genomes botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens Bacillus 4 16 25 41 and Entamoeba histolytica. Each pathogen is represented in one of four distinct clade-specific Pathema web resources developed to target the data and analysis Burkholderia 5 21 8 29 needs of each scientific community. Included in these resources is a customized Clostridium 7 15 35 50 suite of sophisticated bioinformatics software, an extensive library of literature and Detailed manually curated data, and comparative analysis tools customized to retrieve, Entamoeba 3 0 0 3 Strain display, and compute results relevant to ongoing bio-defense research. Curated Total 19 52 68 123 Information datasets of clade-specific virulence factors, epitopes, and toxins, as well as bioinformatics tools for cross genome comparisons, identification of metabolic pathways, and SNP analysis were integrated into Pathema to facilitate the Pathogenicity identification of potential targets for vaccine development, therapeutics, and diagnostics. The overarching goal of Pathema is to provide core resources that will accelerate scientific progress on understanding, detecting, diagnosing and treating Category A-C pathogens and other pathogens involved in new and re-emerging JCVI Curated: infectious diseases. There are no license restrictions for user access to this data  Virulence Factors and all source code for Pathema is managed under an open-source collaborative development paradigm. In addition, clade-specific training courses are offered to provide instruction on the use of this system and the underlying databases. Pathema serves as a focal point for the bio-defense research community by disseminating data resulting from bacterial genome sequencing projects and providing access to the results of inter-genomic comparisons.  Clostridum Toxin Database Functional Genomics Genome Properties KEGG Pathways  PFGRC Microarray Requests Functional Curation Comparative Analysis  Community Annotation Tool Positional Best Protein Hits Multi-Genome Homology  Experimentally Characterized Protein List Comparison Genome Region Comparison Community Outreach Individual Gene Pages  Data exchange & integration Genome sequence analysis  Custom data analysis Custom tool development  Pathema & annotation training Contact: