Question: Genbank Annotation Liftover Between Prokaryote Genomes
1
gravatar for Martin A Hansen
7.6 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

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

annotation genbank • 1.9k views
ADD COMMENTlink written 7.6 years ago by Martin A Hansen3.0k
1
gravatar for lexnederbragt
7.6 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

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/

ADD COMMENTlink written 7.6 years ago by lexnederbragt1.2k
0
gravatar for Istvan Albert
7.6 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

http://biostar.stackexchange.com/page/search

ADD COMMENTlink written 7.6 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Martin A Hansen
7.6 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

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.

ADD COMMENTlink written 7.6 years ago by Martin A Hansen3.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1169 users visited in the last hour