WormBase ParaSite − a comprehensive resource for helminth genomics

TLDR

Publicly available parasitic worm genome sequences have surged in the past three years, and systematic organization, curation, analysis, and presentation of these data are essential for maximizing their research utility. The review outlines the back‑end infrastructure and analysis of WormBase ParaSite and the tools that allow users to interrogate helminth genomic data. WormBase ParaSite integrates data from more than 100 nematode and platyhelminth species, providing systematic functional annotation, gene‑expression and comparative analyses, and offers genome browsers, summary pages, search tools, a query wizard, bulk downloads, and programmatic interfaces. The portal WormBase ParaSite enables large‑scale interrogation of helminth genomes.

Abstract

The number of publicly available parasitic worm genome sequences has increased dramatically in the past three years, and research interest in helminth functional genomics is now quickly gathering pace in response to the foundation that has been laid by these collective efforts. A systematic approach to the organisation, curation, analysis and presentation of these data is clearly vital for maximising the utility of these data to researchers. We have developed a portal called WormBase ParaSite (http://parasite.wormbase.org) for interrogating helminth genomes on a large scale. Data from over 100 nematode and platyhelminth species are integrated, adding value by way of systematic and consistent functional annotation (e.g. protein domains and Gene Ontology terms), gene expression analysis (e.g. alignment of life-stage specific transcriptome data sets), and comparative analysis (e.g. orthologues and paralogues). We provide several ways of exploring the data, including genome browsers, genome and gene summary pages, text search, sequence search, a query wizard, bulk downloads, and programmatic interfaces. In this review, we provide an overview of the back-end infrastructure and analysis behind WormBase ParaSite, and the displays and tools available to users for interrogating helminth genomic data.