Protists

Release Intentions

  • New genomes
    • New load of protist genomes from ENA
  • New data
    • Automated RNA gene annotation update
  • Updated data
    • Updated PHI-base 4.3 annotations
    • Updated protein features
    • Updated BioMarts

Release Notes (Brief)

​New genomes have been loaded from INSDC, and included in compara. New automatic ncRNA alignments have been added across all protists, using a new algorithm that aims to minimise false positive results by applying taxonomic (and other) filters. Cross references to other resources (such as UniProt and RefSeq) have been updated. Updated phenotypic information from PHI-base 4.3 have been added for phytopathogenic species.

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What's New in Release 37

  • Genomes
    • 189 genomes from 119 species
    • 4 new genomes added, 3 genomes renamed and 130 genomes have updated annotation since release 36
  • New data
    • New automatic ncRNA alignments across all protists
  • Updated data
    • Updated phenotypic annotation from PHI-base 4.3
    • Updated protein features
    • Updated BioMarts

Future Releases

Ensembl Protists

Ensembl Protists is a browser for protist genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators.

Data access

Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats.

New Ensembl Genomes Archive Sites

Ensembl Genomes now has archive sites for all divisions. These can be found at the following URLs:

http://oct2017-metazoa.ensembl.org

http://oct2017-plants.ensembl.org

http://oct2017-fungi.ensembl.org

http://oct2017-protists.ensembl.org

http://oct2017-bacteria.ensembl.org

The archive sites will allow researchers to access data from old releases in our web-based tools, and additionally will be able to display track hubs containing alignments and features located on older versions of genome assemblies that have since been upgraded in the live site. Archive sites will be searchable and BioMarts will be available where they were produced for the site when live. Schema and API versions for archive sites will be the same as when the data was released, i.e. archive sites will not be updated to use the most recent versions. Ensembl tools will not be active in the initial release, but we are hoping to enable these shortly. Major bugs (i.e. those impeding the usability of the site) will be fixed, but minor bugs will not be.

The first release of the archive sites contains content from release 37. New archive sites will be released at least once a year, under URLs indicating the date of first release of the data they contain. The previously existing archive for Ensembl Plants, http://archive.plants.ensembl.org, will continue to be available at this URL, but also as http://mar2016-plants.ensembl.org, in accordance with the new naming scheme. As previously, data from all recent releases will continue to be available for download at ftp://ftp.ensemblgenomes.org.

PhytoPath

PhytoPath is a joint project between EMBL-EBI and Rothamsted Research, funded by the BBSRC, linking genomic and phenotoypic data of fungal and oomycete plant pathogens.

BBSRC Logo PhytoPath is funded by the BBSRC.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.