| title | description | published | date | tags |
|---|---|---|---|---|
EuPathDB |
The EuPathDB Bioinformatics Resource Center provides a portal for accessing genomic-scale datasets associated with the diverse eukaryotic microbes. |
true |
2020-04-28 11:36:38 UTC |
genomics, tool, sequence analysis, genes, proteins, resource center, database, eukaryotes, transcriptomics, prediction, proteomics, function |
EuPathDB (formerly ApiDB) is an integrated database covering the 405 eukaryotic pathogens listed in their Data Summary page. While these organisms are supported by a taxon-specific database/website built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera. The EuPathDB databases are funded by NIAID and they have strict guidelines as to which organisms they can support. EuPathDB is one of four NIH funded bioinformatics resource centers. Mainly they are to incorporate any eukaryotic pathogen that is deemed emerging or re-emerging. They also have some organisms that are not on the list, those were either added in the past on the behest of the community and additional funding (such as TrichDB), organisms that are related to emerging or re-emerging pathogen (such as Plasmodium or Neospora) and the trypanosomatids (funded as a pilot project by the Bill and Melinda Gates foundation). The EuPathDB family of databases is expected to expand further over the coming years, incorporating new species including the Amoebozoa (Entamoeba, Acanthamoeba), Microsporidia, and additional Apicomplexans, Kinetoplastida and Diplomonads. Of course, they continue collecting data that are being deposited at an ever-increasing rate, including additional genome sequences, microarray data, probe-based hybridization and sequencing data (e.g. ChIP-chip and RNA-Seq), proteomics data, isolate data, phenotype information and metabolomic data. {.is-info}
- EuPathDB Main Page {.links-list}
- Users personal experimental data (RNA-seq, ChIP-seq, Variants, etc) can be analyzed using the free EuPathDB-dedicated Galaxy site, preloaded with EuPathDB genomes and workflows and hosted by Globus Genomics.
- The database assists users to easily create and save multi-step search strategies which could be very convenient for publishing and teaching purposes.
- EuPathDB: the eukaryotic pathogen genomics database resource. Cristina Aurrecoechea; Ana Barreto; Evelina Y. Basenko; John Brestelli; Brian P. Brunk; Shon Cade; Kathryn Crouch; Ryan Doherty; Dave Falke; Steve Fischer; Bindu Gajria; Omar S. Harb; Mark Heiges; Christiane Hertz-Fowler; Sufen Hu; John Iodice; Jessica C. Kissinger; Cris Lawrence; Wei Li; Deborah F. Pinney; Jane A. Pulman; David S. Roos; Achchuthan Shanmugasundram; Fatima Silva-Franco; Sascha Steinbiss; Christian J. Stoeckert Jr; Drew Spruill; Haiming Wang; Susanne Warrenfeltz; Jie Zheng. Nucleic Acids Research 2017 doi: 10.1093/nar/gkw1105 {.grid-list}