This week, Albert Vilella and myself participated in the Xfam consortium meeting. The meeting focussed on protein, domains and ncRNA classification, and on the new developments of the HMMER package. Although Ensembl is not part of Xfam, we share many Continue reading Ensembl, Xfam and HMMs
We have added a little trick for orthology-lovers. Starting from the orthologues page, you can choose to switch to the GeneTree. This will highlight the orthologue of interest, as well as the ancestral node that relates both genes. Another useful Continue reading Orthologues on the trees
Ensembl 57 includes the turkey genome, the third bird in Ensembl. We are now providing a 3-way avian multiple alignments (chicken, turkey and zebra finch) together with GERP constraint analysis. The image shows amniote and bird constrained elements on the Continue reading New avian and new fish mutliple alignments
The gene tree images now have little intron “ticks” on them showing how the intron position is placed relative to the protein sequence. An example is shown above. Each tick is a little black line on each side of the Continue reading Gene Trees now have intron ticks.
When we changed our look and feel almost a year ago, we “left behind” our two main graphical genome-wide comparative genomics displays (our textual comparative genomics displays remains, as did some of the gene centric ones). These were some of Continue reading Genome-wide comparative displays
Release 55 has lots of goodies – not least the new, coordinated, GRCh37 assembly (more on that later), but one addition is the Martability of Ensembl Regulatory Features. Regulatory features are on by default on Human and Mouse, and each Continue reading Ensembl Regulatory Features – now Martable
We have some news for the forthcoming ensembl release. We have added a few more display options for our gene trees. It will be possible to colour the background of the trees based on the taxonomy. It will be much Continue reading Colourful gene trees
The new Ensembl release includes a new view for SNPs and other genomic variations. It shows the alignment of the polymorphic position together with 10 base pairs of sequence up- and downstream. The user can choose among all available multiple Continue reading SNPs and ancestral alleles
Many users ask us about how to download data from ensembl. Usually, the answer is using BioMart. Comparative genomics data are also available in the standard Mart for your favorite species. For instance to get all the human-mouse orthologs, one Continue reading How to get all the orthologous genes between two species
If you have clicked on the GeneTree link in Ensembl (for example, the gene tree for IL2), you may have noticed that we have a new way of displaying large GeneTrees. This time, if you have a large gene family Continue reading GeneTrees: how do I read them? And can I view alignments using Jalview?