What's New in Release 38
- No significant updates to fungal genomes
- Updated data
- New references to the Rhea database linked to EC (Enzyme Commission) numbers in fungi
- Updated protein features for all fungal peptides
- Updated BioMarts
Ensembl Fungi is a browser for fungal 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.
Advanced Course on Fungal Pathogen Genomics
A Wellcome Trust Advanced Course on Fungal Pathogen Genomics will take place from 13th-18th May 2018, Hinxton, Cambridge. This course provides hands-on training on how to take advantage of unique tools offered by a number of leading fungal databases, including Ensemb Fungi, to develop testable hypotheses, and interrogate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces. Daily activities at the workshop will include individual and group hands-on training exercises, supplementary lectures on bioinformatic techniques and tools used by various databases, and presentations by distinguished guest speakers. Follow the link to learn more and apply for your place!
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.