Comparing genome assemblies

Question

[xandinho2468]

I have a list of Refseq IDs from Vv genome that came from a Pullseq analysis experiment. I need to convert them to ensemble ID that comes from the consortium. I the past I used GFFcompare to retrieve the list but in this case now only the NCBi reference is different but also the number of predicted genes is different.

Is there a way to compare the two assemblies or to "translate" the coordinates from one ref to the other?

[GenoMax]

What is Vv genome? You know but we don't :-)

[Naresh]

Vv genome means - vaccinia virus genome???

[xandinho2468]

Vitis vinifera. sorry!!!

[GenoMax]

If the assemblies are different then short of doing alignments it would not be possible to translate the coordinates directly (unless Ensembl or NCBI has already done this step).

Answer 1

[Denise CS]

The chances are that the RefSeq IDs will be the same across the two assemblies. The coordinates of the genes will change when comparing two assemblies, A and B. But it's unlikely new IDs will be given to the same gene in the two different assemblies. So if you have a list of RefSeq IDs e.g. NM_001281185, you can convert them into Ensembl IDs using BioMart in Ensembl Plants. If you are completely new to BioMart have a look at our latest video and tutorials. If you want to convert the coordinates of these IDs from one assembly to another in V vinifera, give our assembly converter a try.