VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Abstract

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

“…[47][48][49][50][51]), and scalable pipelines for the construction of many networks (i.e. CarveMe [52], ModelSEED [53]), we sought to build on these tools and the Eukaryotic Pathogens Database (EuPathDB [54]) to leverage genomic information on the EuPathDB database and existing effort towards manual curation of individual reconstructions.…”

“…To build a comprehensive collection of genome-scale network reconstructions representing parasite metabolism, we designed a novel network reconstruction pipeline optimized for eukaryotic organisms (Fig2A). Our pipeline builds on publicly available, open source software and resources[52,[54][55][56] and focuses on the compartmentalization of biochemical reactions (Fig2A). We applied this pipeline to assemble networks for all publicly available reference genomes from parasite isolates representing 119 species (see Data Availability for link to code…”

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…The well-known PHI-BASE reports ( 62 ) new pathogens and hosts, and describes the range of other databases to which it contributes annotations. The second, VEuPathDB ( 63 ), is a new name to the Issue but contains genomic and a wide variety of other information on eukaryotic pathogens, their vectors and host, information previously stored in its parent databases VectorBase ( 64 ) and EuPathDB ( 65 ), each published here. The site allows construction of sophisticated search strategies and options for analysing host-pathogen interactions are a future priority.…”

An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease

“…The alignments were tabulated using samtools mpileup ( Li et al., 2009 ) and variant loci were identified using VarScan2 software ( Koboldt et al., 2012 ). Genomic locations of SNPs and enrichment analyses were performed using TriTrypDB ( Amos et al, 2022 ).…”