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ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms

  • Omar S. HarbEmail author
  • David S. RoosEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2071)

Abstract

ToxoDB is a free online resource that provides access to genomic and functional genomic data. All data is made available through an intuitive queryable interface that enables scientists to build in silico experiments and develop testable hypothesis. The resource contains 32 fully sequenced and annotated genomes, with genomic sequence from multiple strains available for variant detection and copy number variation analysis. In addition to genomic sequence data, ToxoDB contains numerous functional genomic datasets including microarray, RNAseq, proteomics, ChIP-seq, and phenotypic data. In addition, results from a number of whole-genome analyses are incorporated including mapping to orthology clusters which allows users to leverage phylogenetic relationships in their analyses. Integration of primary data is made possible through a private galaxy interface and custom export tools that allow users to interrogate their own results in the context of all other data in the database.

Key words

ToxoDB EuPathDB Apicomplexa Genomics Database Bioinformatics 

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Authors and Affiliations

  1. 1.Lynch Laboratories, Department of BiologyUniversity of PennsylvaniaPhiladelphiaUSA

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