EuPathDB: The Eukaryotic Pathogen Genomics Database Resource

  • Susanne Warrenfeltz
  • Evelina Y. Basenko
  • Kathryn Crouch
  • Omar S. Harb
  • Jessica C. Kissinger
  • David S. Roos
  • Achchuthan Shanmugasundram
  • Fatima Silva-Franco
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1757)

Abstract

Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen’s biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources (http://eupathdb.org) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpathogenic species. EuPathDB integrates preanalyzed data with advanced search capabilities, data visualization, analysis tools and a comprehensive record system in a graphical interface that does not require prior computational skills. This chapter describes guiding concepts common across EuPathDB sites and illustrates the powerful data mining capabilities of some of the available tools and features.

Key words

Bioinformatics Parasite Pathogen Genomics Transcriptomics Orthology Fungi Proteomics Sequence analysis 

Notes

Acknowledgments

EuPathDB would like to acknowledge their current funders, the National Institutes of Health (USA), the Wellcome Trust (UK), as well as past funders and The Bill and Melinda Gates Foundation (USA), The Burroughs Wellcome Fund (USA).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Susanne Warrenfeltz
    • 1
  • Evelina Y. Basenko
    • 2
  • Kathryn Crouch
    • 3
  • Omar S. Harb
    • 4
  • Jessica C. Kissinger
    • 1
    • 5
    • 6
  • David S. Roos
    • 4
  • Achchuthan Shanmugasundram
    • 2
  • Fatima Silva-Franco
    • 2
  1. 1.Center for Tropical and Emerging Global DiseasesUniversity of GeorgiaAthensUSA
  2. 2.Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
  3. 3.Wellcome Trust Centre for Molecular ParasitologyUniversity of GlasgowGlasgowUK
  4. 4.Department of BiologyUniversity of PennsylvaniaPhiladelphiaUSA
  5. 5.Institute of BioinformaticsUniversity of GeorgiaAthensUSA
  6. 6.Department of GeneticsUniversity of GeorgiaAthensUSA

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