May was a very busy month for Ensembl Outreach. Besides our customary user support activities, in 14 days, I crisscrossed the east coast of the US, attended the Biology of Genomes conference at CSHL and gave six Ensembl browser workshops at NIH-NHGRI, NIH-NIEHS and UNC-Chapel Hill.
One attendee answered our standard feedback question “Will you use Ensembl more often after this workshop?” with “Absolutely. This is the place!”
So you may wonder: the place? For what?
Well, where should we start?
Maybe with one of the best known aspects of Ensembl: our in-house gene annotation pipeline available for more than 65 vertebrates, including our popular human, mouse and zebrafish genomes. For these three species, the Havana group also contributes manual gene annotation and, in human, the combination of the Ensembl automatic pipeline and the Havana manual annotation gives rise to the merged gene set GENCODE.
But there is much more.
Ensembl is also the place for a wealth of variation data, whose effects on genes, transcripts and proteins (e.g. amino acid changes, premature stop codons, etc) are available. You can also calculate the effect of your own variants on a transcript using VEP.
Ensembl is the place for protein-coding and ncRNA gene trees, whole genomic alignments and synteny.
It is where you can get regulatory data based on the ENCODE and Roadmap projects.
You can also visualise your BAM files from sequencing reads or display your variant calls from your variation studies.
Frequent Ensembl APIs users can subscribe to our developers list.
All Ensembl users can ask us any question at the helpdesk.
Let us know if Ensembl is the place for you too!