How To Display Old Assemblies Of The Mouse Genome In The Ensembl Genome Browser

Question

[Anima Mundi]

Hello,

I would like to know how to display old assemblies of the mouse genome (such as mm7) in the Ensembl Genome Browser. I saw it is possible to download old genomic versions as FASTA, but I would prefer to directly visualize them if possible.

Answer 1

[Neilfws]

In the footer of Ensembl pages, e.g. this one for Cntnap1, is a link that says "View in archive site."

However, the archives only go back so far; Ensembl 54 (May 2009) in this case. I don't know how that relates to e.g. mm7, but I don't think it's possible to view older assemblies.

[Obi Griffith]

The current version of mouse in Ensembl (release 68) corresponds to GRCm38 (mm10). The Ensembl versions still available by archive at this time (release 67 back through release 54) correspond to NCBIM37 (mm9). You can still go back to mm7 in the UCSC genome browser. It is also probably theoretically possible to set up or find someone who has set up their own instance of Ensembl and has the old mm7 releases downloaded. However, that's getting quite out of date so your plan to just update your data to mm10 is probably the best.

[Anima Mundi]

Thanks a lot. That was my fear, I will have to move my data to mm10 then.