Question: Regarding Annotation Of Available Genomes On Jgi
0
gravatar for Kits
7.0 years ago by
Kits30
Kits30 wrote:

I have found that JGI provides completed sequencing of many genomes with annotation (http://genome.jgi-psf.org/ChlNC64A_1/ChlNC64A_1.download.ftp.html). However I have some questions regarding file format. They provide Assembly, Annotation files but there is no single file which contains the complete genome of particular organism like NCBI provides various standard formats like .FNA and .GBK

My question: 1) Where to find complete genome sequence of respected organism in ".FNA' format? 2) Where can i find complete annotated format of particular genome in ".GBK OR.GB" format ? 3) If .fna and .gbk file is not available, how can I generate .gbk file and .fna file from available data? Please inform or suggest options for me regarding this issue.

annotation • 3.1k views
ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Kits30

That link returns "Your are not logged in and requested resource or function requires authorization." Which organism is it? Is it a private resource?

ADD REPLYlink written 7.0 years ago by Neilfws48k
2
gravatar for Josh Herr
7.0 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

Basically all JGI genome information is available to you in the format you can use. You really need to get a clue about what file formats you need and why you need them in that format. You haven't given us any information to help you on.

You are looking for a FASTA file for your .FNA file. All the files through JGI are in this format, but they may be .txt or .fa when you download them. They will also be tarballed, so you will have to unzip them first.

All the JGI annotation files (to my knowledge) are in .GFF format. If you absolutely need files in Genbank format then you need to convert them. This is pretty easy to do. Are you sure you need the annotation files in Genbank format?

You didn't specify which organism you are looking to download, so we can't help you there. Much of JGI's data is available through the biomart portal.

In the future, please reference this article before you post.

ADD COMMENTlink written 7.0 years ago by Josh Herr5.6k
0
gravatar for Kits
7.0 years ago by
Kits30
Kits30 wrote:

Thanks for reply, I am looking for particular for algae (Chlorella NC64A) full genome in fasta format and annotation files in Genbank format but there are files provided in .gff (for genes), .tab (gene annotation) and .fasta (scaffold file of assembly) on JGI . How to make single fasta file from available scaffold file and annotation files like genebank file(.gbk) ?

ADD COMMENTlink written 7.0 years ago by Kits30
1

Next time add your clarifications to the comments section of your original post. Thanks!

ADD REPLYlink written 7.0 years ago by Josh Herr5.6k
0
gravatar for Josh Herr
7.0 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

Ok, you still haven't given us very much information, but since you are looking at Chlorella variabilis, you can FTP the whole genome sequence here. Do you need the masked version or the unmasked version of the assembly? I still can't understand what you actually want to do: Do you know what you want to do and why you want to do it?

The genome is in the form of numerous contigs in a single file. Isn't that what you are looking for? You keep saying you need a genbank file, why do you need this and what are you doing with it? If you give us this information, we can try to help you.

ADD COMMENTlink written 7.0 years ago by Josh Herr5.6k

I have two main objective ,First is comparison of whole genome of Chlorella variabilis to another complete genome of Bacteria .Another genome file downloaded from (http://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/) Second,analysis of pathway between two organism with annotation information available on .gbk file. can we make single contig from numerous contigs available in masked data?

ADD REPLYlink written 7.0 years ago by Kits30
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