Genbank File generation

Question

[utkarsh.sood]

Hi

I have a newly sequenced bacterial genome and I want to do SNP analysis among the strains of that bacterial species using GET_Homologues. For this I require a Genebank file as accurate as generated by NCBI. Is it possible to generate a Genebank file as accurate as generated by NCBI without uploading the genome on NCBI?

Answer 1

[emmanuel.bouilhol]

Hi,

I think you will have some answers here: http://www.ncbi.nlm.nih.gov/genbank/submit

As far as I know, you can create a Genbank file with submition tools without uploading it, look at "Confidentiality" paragraph.

Answer 2

[aleimba]

Hi,

"as accurate" is a bold statement in annotation. But there are lots of tools out there (online or local) for annotation. For prokaryotic genomics, which I'm guessing you want to do, the most common ones are:

• Prokka (http://www.vicbioinformatics.com/software.prokka.shtml)
• RAST (http://rast.nmpdr.org/)
• JGI's IMG-ER (https://img.jgi.doe.gov/cgi-bin/mer/main.cgi)
• The aforementioned NCBI PGAAP (Prokaryotic Genome Annotation Pipeline, http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) pipeline.

Also, get_homologues is a tool for homolog/ortholog detection and clustering. Unless I'm missing something, its purpose is not SNP calling.

HTH