Question: How To Display Old Assemblies Of The Mouse Genome In The Ensembl Genome Browser
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gravatar for Anima Mundi
6.7 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Anima Mundi2.4k
1
gravatar for Neilfws
6.7 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Neilfws48k
1

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 However, that's getting quite out of date so your plan to just update your data to mm10 is probably the best.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Obi Griffith17k

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

ADD REPLYlink written 6.7 years ago by Anima Mundi2.4k
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