Genbank Annotation Liftover Between Prokaryote Genomes
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10.7 years ago

I would like to create a GenBank file with annotations for the complete genome of organism A (prokaryote) using the existing GenBank file from organism B. The only difference between A and B is a small number of sequence regions have been deleted from A. Is there any tool out there that can do this?

Cheers

Martin

genbank annotation • 2.5k views
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10.7 years ago
lexnederbragt ★ 1.3k

Looks like RATT (Rapid Annotation Transfer Tool) could do what you need:

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

http://ratt.sourceforge.net/

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10.7 years ago

Possibly the easiest way to accomplish your task would be to use an aligner to remap the sequences that correspond to the annotations from organism A to organism B.

This is a fairly common need so you should also use the custom search with the word liftover

https://www.biostars.org/local/search/page/

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10.7 years ago

I found another possible answer. That is to upload the genome of organism B to RAST where organism A is already included. I will update this answer when I have finished testing.

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