EuPathDB: the eukaryotic pathogen genomics database resource

Abstract

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions.

Direction of flagellum beat propagation is controlled by proximal/distal outer dynein arm asymmetry

“…Quantity of IFT (T) was initially set to 0.2 /interval, assuming around 5 IFT trains per second (78) The localisations of the T. brucei docking complex proteins were initially identified from TrypTag.org (41). T. brucei and L. mexicana protein and genome sequences were accessed using TriTrypDB.org (79). L. mexicana orthologs of T. brucei proteins were identified using synteny and orthogroup data from TriTrypDB.org (79), and manually confirmed by reciprocal best BLAST.…”

“…T. brucei and L. mexicana protein and genome sequences were accessed using TriTrypDB.org (79). L. mexicana orthologs of T. brucei proteins were identified using synteny and orthogroup data from TriTrypDB.org (79), and manually confirmed by reciprocal best BLAST. C. reinhardtii, G. lamblia and human orthologs were identified using orthogroups as found by orthofinder(80) run on 45 diverse eukaryote genomes, then manually checked by BLAST search.…”

Natural infection with Giardia is associated with altered community structure of the human and canine gut microbiome

“…5A and 5B) from over 22,000 participants. These data were manually 174 combined with fecal microbiome data from a subset of the same participants (n=1004), 215 of 175 whom were positive for Giardia, which was loaded on MicrobiomeDB.org (29,30). Not 176 surprisingly, age and moderate-to-severe diarrhea (MSD) were strongly correlated with Bray-177…”

“…The Global Enteric Multicenter Study (GEMS) investigated the causes, incidence, and 320 impact of moderate-to-severe diarrhea in 23,567 0-59 month-old children in Asia and Africa 321 (27). Clinical and epidemiological data, and anthropometric measurements for each participant 322 were downloaded from ClinEpiDB.org (29,30). The presence of Giardia, Cryptosporidium, and Rotavirus were determined using an antibody-based ELISA test on participant fecal samples.…”

State‐of‐the‐art CRISPR/Cas9 Technology for Genome Editing in Trypanosomatids

“…This research group also developed an online tool for sgRNA design, named Eukaryotic Pathogen CRISPR guide RNA/DNA Design Tool (Peng and Tarleton ), which is very useful for off‐target analysis in the genomes of kinetoplastids or any organism of the EupathDB database (Aurrecoechea et al. ), and also allows custom genome upload.…”