Gene Annotation Transfer: Ensembl To A Novel Assembly

Question

[Darked89]

Bovine genome is already in ENSEMBL 61 and was annotated using the whole ENSEMBL annotation pipeline. Problem is, version of the genome used by ENSEMBL (lest call it A) is dated, and newer assembly (B) using exactly the same genomic DNA is available. While B is also annotated using Gnomon pipeline I want to be able to compare annotations and use ENSEMBL gene ids.

Since it will be months until B may be incorporated in ENSEMBL, I want to use B but with annotations without rerunning the whole annotation pipeline.

So my question is:

what is the best (or a t least sensible...) way to get gene annotations from one assembly mapped to another?

edit: changed assembly symbols (A=old, B=new) for clarity.

[Michael Kuhn]

Do you mean "annotation" as in "finding proteins" or as in "assigning names to proteins"?

[Darked89]

"annotation" as "describing chunks of DNA sequence as exons of a gene". Also "if gen X has following coordinates on genome assembly A, what are gene X coordinates on genome assembly B". Lastly, at this stage I am not interested in improving existing annotation for gene X. If it does miss an exon or two on assembly A, so be it, even if this region is present in assembly B.

Answer 1

[Scott Cain]

I would suggest you look at MAKER.

It has functionality specifically for migrating annotations from one assembly to another.

[Gvj]

Could you please specify which function/script you are mentioning ?