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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Entering edit mode
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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Entering edit mode
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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Entering edit mode
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.