New Oyster assembly available
Like Trey, I have been poking around at the new Ensembl version. We’ll have to update our tutorial to reflect the changes, of course. However, there are reasons to maintain the previous tutorial version in some form as well. Ensembl maintains archives where you can look back at previous data and the old version of the software persists. This can be handy if you are seeing something in a publication that refers to a previous assembly/version.
Some sites may use Ensembl software and may not migrate to the new interface–or if they will, it could take significant time. An example of this is the Farm Animal Genome Database, or the SIGENAE: the Information System of the AGENAE program. More about AGENAE here.
I was checking out their site to see if they mentioned that they would move to the new Ensembl style. I don’t see any indication of that right now. The current news is the updated Oyster browser assembly. So they appear to be updating the data but using the previous Ensembl software. There are a number of genomes here that you might want to examine if your genomic interests include farm species: pig, chicken, cattle, rabbit, sheep and a number of fish. But I was previously unaware of the oyster browser.
Software versions change, but previous versions may also persist for quite a while. And it is handy to know how to use the older ones sometimes.