This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genbank Annotation Liftover Between Prokaryote Genomes

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
• 3,540 views • link
written by Martin A Hansen 305

3 answers

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/

• 0 views • link
written by lexnederbragt 128

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/

• 2 views • link
updated by Ram 4.5K • | written by Istvan Albert 10K

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.

• 1 views • link
written by Martin A Hansen 305

Log in to answer this question.

More posts like this