How to Modify Reference Sequence and Annotation Files

Question

[LDT]

Dear all,

I have edited in the lab a bacterial genome -i.e, I have added an antibiotic cassette which is around 500bp.

Now I want to edit it in the computer, update the fasta file, the gff and then export it to .gbk and use for SNP calling in Breseq.

How do I edit the genome? Any idea?

[yeastbuddy]

Hey, any idea how you did this in the end? I need to do this now too

Answer 1

[lieven.sterck]

if it's only for this one time (or limited number of times) best and most easy is to do this manually.

1. Open your sequence & annotation file in a genome-editing tool, eg. jBrowse, Apollo, IGV(?), artemis, Genomeview, ...
2. make your edit to the genome
3. save your fasta and annotation file
4. export in desired output format.

Normally if you make the edit the annotations will change accordingly (and especially so if you change it in a non genic region, genic regions might be a bit more cumbersome).

Perhaps not all of those browsers I mentioned do allow to edit the genome sequence though (this is rather a special feature of some of those) but among that list there should be some that can do this.