Search for a gene
Search for a genome
e.g. type pla to find Plasmodium
What's New in Release 39
- 189 genomes in total from 119 species
- Updated genomes
- Toxoplasma gondii ME49 (annotation from ToxoDB release 36, assembly GCA_000006565.2)
- Updated data
- Updated compara for 118 species
- Updated protein domain information based on latest InterProScan
- Updated BioMarts
- Known issues in protist compara (to be fixed for next release):
- Leishmania major genes are not included in gene trees; consequently, there are no L. major homologues
- The version of Toxoplasma gondii in gene trees and homologies is not the new 'ME49' strain (assembly version TGA4), but is the 'VEG' strain (assembly version TGVEG)
- Pairwise alignments are missing for:
- Leishmania major
- Toxoplasma gondii
- Please see our archive site for a previous version of these data sets
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 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:
The archive sites will allow researchers to access data from old releases via 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; likewise, archival REST servers will not initially be available, but will be added in future. 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 is funded by the BBSRC.|