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Protocols

EuPathDB specifications

Information


Unique identifier OMICS_03154
Name EuPathDB
Alternative names ApiDB, EuPathDB-clean
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Allowed
Version 37
Maintained Yes

Taxon


  • Invertebrates
    • Giardia intestinalis
    • Leishmania major
    • Plasmodium falciparum
    • Toxoplasma gondii
    • Trichomonas vaginalis
    • Trypanosoma brucei
  • Plants and Fungi
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe

Documentation


Maintainers


  • person_outline Omar S. Harb
  • person_outline Susanne Warrenfeltz

Additional information


A clean version of this resource is available as EuPathDB-clean at http://ccb.jhu.edu/data/eupathDB/ and the associated publication is available as https://doi.org/10.1101/261859.

Publications for EuPathDB

EuPathDB citations

 (40)
library_books

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] iza Hall Institute for Medical Research Systems Biology Mascot Server) against the non-redundant MSPnr100 database compiled from all known reference protein sequences including NCBI, Refseq, UniProt, EuPathDB and Ensembl. Peptides matches at p < 0.05 (Ion score > 60) were classified as hits. […]

library_books

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

2018
PMCID: 5872342
DOI: 10.3390/jof4010039

[…] EuPathDB Galaxy-based [] workspace offers preloaded genomes, private data analysis and display, and the ability to share and export analysis results []. Developed in partnership with Globus Genomics [ […]

library_books

ROP: dumpster diving in RNA sequencing to find the source of 1 trillion reads across diverse adult human tissues

2018
Genome Biol
PMCID: 5857127
PMID: 29548336
DOI: 10.1186/s13059-018-1403-7

[…] collection of bacterial, viral, and eukaryotic reference genomes. Bacterial and viral genomes were downloaded from NCBI (ftp://ftp.ncbi.nih.gov/). Genomes of eukaryotic pathogens were downloaded from EuPathDB (http://eupathdb.org/eupathdb/). We used MetaPhlAn2 (Metagenomic Phylogenetic Analysis, v 2.0) to obtain the taxonomic profile of microbial communities present in the sample.Quality control. […]

library_books

The Ancient Link between G Protein Coupled Receptors and C Terminal Phospholipid Kinase Domains

2018
MBio
PMCID: 5784254
PMID: 29362235
DOI: 10.1128/mBio.02119-17

[…] he supplemental material). Protein sequences of previously annotated GPCR-PIPKs (, ) were used as queries for BLAST searches (E value cutoff score of 1 e−1) against the NCBI, UniProt, FungiDB (), and EuPathDB databases () (last accessed 5 May 2017). These databases cover proteomes of a wide range of species, including archaea, bacteria, and organisms from all eukaryotic supergroups. In parallel, H […]

call_split

N terminomics identifies widespread endoproteolysis and novel methionine excision in a genome reduced bacterial pathogen

2017
Sci Rep
PMCID: 5593965
PMID: 28894154
DOI: 10.1038/s41598-017-11296-9
call_split See protocol

[…] by the 6600 TripleTOF were searched using Mascot Daemon (version 2.4; Perkins, D.N. 1999) against the MSPnr100 database (based on the major reference sequence repositories of NCBI, Refseq, UniProtKB, EupathDB and Ensembl. Duplicate entries at the species-level are removed, “multispecies” entries (NCBI) and “fragments” (TrEMBL) are ignored. vQ115). The search parameters were: Precursor tolerance 10 […]

library_books

Genome wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors

2017
Sci Rep
PMCID: 5469757
PMID: 28611446
DOI: 10.1038/s41598-017-03445-x

[…] urces of evidence-based prediction on the Maker2 pipeline, on ab initio gene predictor algorithms with P. falciparum 3D7, B. bovis T2Bo, and T. annulata Ankara gene models as templates retrieved from EuPathDB release 26, and on Trinity-assembled de novo transcriptome evidence. Repetitive genomic elements were identified and masked from annotation with RepeatMasker using the full Repbase database. […]

Citations

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EuPathDB institution(s)
Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK; Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK; Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Department of Genetics, University of Georgia, Athens, GA, USA
EuPathDB funding source(s)
Supported by the National Institutes of Health (USA), the Wellcome Trust (UK), as well as past funders and The Bill and Melinda Gates Foundation (USA), The Burroughs Wellcome Fund (USA).

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