pathema: a bioinformatics resource center

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 Community Annotation Tool Experimentally Characterized Protein List Functional Curation Individual Gene Pages Comparative Analysis Multi-Genome Homology Comparison Genome Region Comparison Positional Best Protein Hits Clostridum Toxin Database JCVI Curated: Virulence Factors Pathogenicity Data exchange & integration Genome sequence analysis Custom data analysis Custom tool development Pathema & annotation training Contact: [email protected] Community Outreach Genome Properties KEGG Pathways Functional Genomics Pathema Organisms Genome Graphical Displays Detailed Strain Information Available Genomes Pathema (http: //pathema . jcvi .org ) is a NIAID Bioinformatics Resource Center designed to support bio-defense and infectious disease research. Pathema provides detailed curation of six target pathogens: Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each pathogen is represented in one of four distinct clade-specific Pathema web resources developed to target the data and analysis needs of each scientific community. Included in these resources is a customized suite of sophisticated bioinformatics software, an extensive library of literature and manually curated data, and comparative analysis tools customized to retrieve, display, and compute results relevant to ongoing bio-defense research. Curated 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 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 infectious diseases. There are no license restrictions for user access to this data 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. Abstract Genus Current # Species Current # Strains Future Genomes Total Genomes Bacillus 4 16 25 41 Burkholderia 5 21 8 29 Clostridium 7 15 35 50 Entamoeba 3 0 0 3 Total 19 52 68 123 PFGRC Microarray Requests

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Page 1: Pathema: A Bioinformatics Resource Center

PATHEMA: A BIOINFORMATICS RESOURCE CENTERLauren Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy*,

Jay Sundaram, Scott Durkin, Owen White*, Granger SuttonJ. Craig Venter Institute, 9704 Medical Center Dr. Rockville, MD, 20850 USA

* Institute for Genome Sciences, 685 West Baltimore St., Baltimore, MD, 21201 USA

Community Annotation Tool Experimentally Characterized Protein List

Functional Curation

Individual Gene Pages

Comparative AnalysisMulti-Genome HomologyComparison

Genome RegionComparison

Positional Best Protein Hits

Clostridum Toxin Database

JCVI Curated: Virulence Factors

Pathogenicity

Data exchange & integration Genome sequence analysis Custom data analysis Custom tool development Pathema & annotation training Contact: [email protected]

Community Outreach

Genome Properties

KEGG Pathways

Functional Genomics

Pathema OrganismsGenome GraphicalDisplays

DetailedStrainInformation

Available GenomesPathema (http://pathema.jcvi.org) is a NIAID Bioinformatics Resource Centerdesigned to support bio-defense and infectious disease research. Pathemaprovides detailed curation of six target pathogens: Bacillus anthracis, Clostridiumbotulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringensand Entamoeba histolytica. Each pathogen is represented in one of four distinctclade-specific Pathema web resources developed to target the data and analysisneeds of each scientific community. Included in these resources is a customizedsuite of sophisticated bioinformatics software, an extensive library of literature andmanually curated data, and comparative analysis tools customized to retrieve,display, and compute results relevant to ongoing bio-defense research. Curateddatasets of clade-specific virulence factors, epitopes, and toxins, as well asbioinformatics tools for cross genome comparisons, identification of metabolicpathways, and SNP analysis were integrated into Pathema to facilitate theidentification of potential targets for vaccine development, therapeutics, anddiagnostics. The overarching goal of Pathema is to provide core resources that willaccelerate scientific progress on understanding, detecting, diagnosing and treatingCategory A-C pathogens and other pathogens involved in new and re-emerginginfectious diseases. There are no license restrictions for user access to this dataand all source code for Pathema is managed under an open-source collaborativedevelopment paradigm. In addition, clade-specific training courses are offered toprovide instruction on the use of this system and the underlying databases.Pathema serves as a focal point for the bio-defense research community bydisseminating data resulting from bacterial genome sequencing projects andproviding access to the results of inter-genomic comparisons.

Abstract

GenusCurrent #

Species

Current #

Strains

Future

Genomes

Total

Genomes

Bacillus 4 16 25 41

Burkholderia 5 21 8 29

Clostridium 7 15 35 50