Question: Getting genbank annotation file from JGI
0
gravatar for bioPiraten
4.3 years ago by
bioPiraten10
Denmark
bioPiraten10 wrote:

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!

genbank gff annotation jgi • 1.9k views
ADD COMMENTlink modified 3.9 years ago by glarue20 • written 4.3 years ago by bioPiraten10
0
gravatar for glarue
3.9 years ago by
glarue20
United States
glarue20 wrote:

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

 

 

ADD COMMENTlink written 3.9 years ago by glarue20
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