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Comparing genome assemblies

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?

genome id
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updated by Denise CS Denise CS • written by xandinho2468 • xandinho2468

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

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written by GenoMax GenoMax

Vv genome means - vaccinia virus genome???

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written by Naresh Naresh

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).

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written by GenoMax GenoMax

1 answer

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.

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written by Denise CS Denise CS

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