title: EuPathDB: the eukaryotic pathogen database.
abstract: EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNA-seq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010.
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Cristina
authors.initials: C
authors.lastname: Aurrecoechea
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authors.initials: A
authors.lastname: Barreto
authors.forename: John
authors.initials: J
authors.lastname: Brestelli
authors.forename: Brian P
authors.initials: BP
authors.lastname: Brunk
authors.forename: Shon
authors.initials: S
authors.lastname: Cade
authors.forename: Ryan
authors.initials: R
authors.lastname: Doherty
authors.forename: Steve
authors.initials: S
authors.lastname: Fischer
authors.forename: Bindu
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authors.lastname: Gajria
authors.forename: Xin
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authors.lastname: Gao
authors.forename: Alan
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authors.lastname: Gingle
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authors.lastname: Grant
authors.forename: Omar S
authors.initials: OS
authors.lastname: Harb
authors.forename: Mark
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authors.lastname: Heiges
authors.forename: Sufen
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authors.lastname: Hu
authors.forename: John
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authors.lastname: Iodice
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Kissinger
authors.forename: Eileen T
authors.initials: ET
authors.lastname: Kraemer
authors.forename: Wei
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authors.lastname: Li
authors.forename: Deborah F
authors.initials: DF
authors.lastname: Pinney
authors.forename: Brian
authors.initials: B
authors.lastname: Pitts
authors.forename: David S
authors.initials: DS
authors.lastname: Roos
authors.forename: Ganesh
authors.initials: G
authors.lastname: Srinivasamoorthy
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.forename: Haiming
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authors.lastname: Wang
authors.forename: Susanne
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authors.lastname: Warrenfeltz
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D010271:Parasites / Q000235:genetics*; D010641:Phenotype; D016792:Piroplasmida / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040901:Proteomics; D040641:Quantitative Trait Loci; D022821:RNA Splice Sites; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D022821:RNA Splice Sites