Since release 81, Ensembl has provided the gene annotations in GFF3 files alongside the already existing GTF ones. While GTF uses its own controlled vocabulary to classify features, GFF3 takes advantage of sequence ontology. In the initial release, we attempted Continue reading GFF3 and Sequence Ontology terms
You may have noticed our beta REST server has been retired. We have replaced it with our new service, http://rest.ensembl.org, and have a handy migration guide to help you update existing scripts. Details about the new server can be found in the article published Continue reading Goodbye REST. Hello REST.
As mentioned in another post, due to the presence of patches in both GRCh37 and GRCh38, the assembly mapping has proven challenging. Related to this, another novelty arises when assigning stable ids to genes. Every time a gene set is Continue reading Maintaining stable ids between GRCh37 and GRCh38
As you may know, the new GRCh38 assembly for human was released in December 2013. This is a major update for Ensembl and will require months of hard work to provide high quality annotation for our users. Our goal is to Continue reading GRCh38 Assembly Mapping – Updating Coordinates in the New Human Genome
The mouse assembly GRCm38 (GCA_000001635.2) was submitted by the Genome Reference Consortium (GRC). The whole assembly comprises 65 toplevel sequences: 19 autosomes, X and Y, 22 unlocalized scaffolds and 22 unplaced scaffolds. These toplevel sequences are assembled from 20,423 contigs Continue reading New Pre! site for Mouse GRCm38