Getting genbank annotation file from JGI

Question

[bioPiraten]

Hi All,

I would like to extract the genbank or (embl) annotation file from genomes sequenced at JGI, which should serve as input for another tool in my analysis pipeline. At JGI you can download the annotation of the genomes in gff format, and you can get the genome or CDS in fasta format.

So my question is:

Is there any way of retrieving the genbank file from jgi or do I have to use a conversion tool to generate the genbank file myself from the gff and fasta files.

If so, which conversion tool would you recommend (I guess people must have had this problem before, so I hope I don't have make a python converter myself)

Thanks!

Answer 1

[glarue]

AFAIK, JGI does not provide data in GenBank format, so you will have to use a tool to convert the FASTA + GFF3 combo to GenBank.

Here is a discussion of one such tool from EMBOSS.

If you're going to be pulling multiple datasets from JGI and you'd like to use the command line, you may find useful a script I wrote to retrieve data from the JGI databases: https://github.com/glarue/jgi-query