Looking for a plant protein? There is now a new fast protein sequence search in Ensembl Plants, using the Hidden Markov Models (using the search tool HMMER). Just click on the 'HMMER' link in the Ensembl Plants banner (or go directly from here), and add your query sequence in plain text or FASTA format.
Gene annotations taken from the pathogen-host interactions database (PHI-base) have been updated to PHI-base version 4.0. Links are provided (from the left hand menu in the gene page) to the new PHI-base website that acomodates detailed information for each annotation. Example: RAT1 in Fusarium graminearum.
Release 27 adds new wheat variation data from the Hapmap project. The data were generated by re-sequencing 62 diverse wheat lines using whole exome capture and genotyping-by-sequencing (GBS). In total 1.57 million SNPs and 162 thousand small indels were identified across the 21 chromosomes of bread wheat. In addition, the genotypes of 475 individuals have been added to the Axiom 820K SNP Array from CerealsDB.
In collaboration with the Ecole Normale Superieure, Paris and the J. Craig Venter Institute, San Diego, we have re-annotated the genome of the marine diatom Phaeodactylum tricornutum. The new annotation was produced using 13,828 non-redundant ESTs, 42 libraries of RNA-Seq generated using Illumina technology and 49 libraries of RNA-Seq data generated under various iron conditions using SoLiD technology, as well as gene models previously predicted in this and related species. The new gene set contains a total of 12,089 protein coding genes, an increase from the 10,402 genes previously predicted. Models have been checked and corrected through a process of manual curation. The gene models have been analysed using InterProScan and Ensembl Compara and are available to explore in Ensembl Protists.
A training course on the Bioinformatics of Plants and Plant Pathogens will be held at EBI from 23rd-25th June, 2016. Please click here for more details and to register.
We're surveying our users to find out more about what you use Ensembl Genomes for, what we do well and what we could do better. The survey should take up only a few minutes of your time, and your answers will be very useful to us: please follow the link to participate https://www.surveymonkey.com/s/HV5T5HZ and feel free to share the link with other users of our service. Thank you!
From release 27 onwards, the Ensembl Genomes BLAST service uses NCBI Blast+ in place of WUBLAST. Please contact us if you have any questions about this change.
The "virtual" mart names used to identify our live BioMarts will change in release 31 to no longer include the version e.g. protists_mart instead of protists_mart_31. This is to make re-use of URLs etc. easier.
As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk).
Shortly before the release 27 of Ensembl Genomes in June 2015, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance.
Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps.
There have been no significant updates for Ensembl Metazoa in this release.
SIFT predictions (incidating the likely impact of amino acid substituions on protein function) have been added to the Ensembl variation database for barley, and can be accessed via the 'Genes and Regulation' pages (example) or the Variant Effect Predictor.