Question: Where is it possible to submit annotated eukaryote genomes?
1
gravatar for Eric Normandeau
3.7 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

I am in the process of preparing a genome and its annotation (in fasta and gff3 format) for submission on NCBI. NCBI is know for its strange formats and I am not excited at the idea of creating the Sequin table for the submission.

It seems the NCBI is the to-go place however, but are there other places to submit an annotated genome where the process may be more streamlined?

submission annotation genome • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Antonio R. Franco4.0k • written 3.7 years ago by Eric Normandeau10k
3
gravatar for Juke-34
3.7 years ago by
Juke-342.2k
Sweden
Juke-342.2k wrote:

You can also submit your annotated eukaryote genome to the European Nucleotide Archive (ENA).

https://www.ebi.ac.uk/ena/submit/genomes

But I guess at the end this will be the same mess to prepare proper flat files of your annotation.

--Update--

NCBI => They describes a a process (in beta version) to create a annotated genome submission from gff3 or GTF here.

ENA => We developed EMBLmyGFF3 allowing to prepare the EMBL flat file ready to submit to ENA from gff3+fasta files.

ADD COMMENTlink modified 17 months ago • written 3.7 years ago by Juke-342.2k

Thank you. I contacted them to ask about the annotation format they require.

ADD REPLYlink written 3.7 years ago by Eric Normandeau10k

I am in the same situation... with a gff3 and fasta file and I would like to prepare the flat file in EMBL format that they require.

C: Emboss seqret - problem conversion gff+fasta to EMBL

For the moment I didn't find any straightforward way that works to do that. So, if you have any information for the conversion I will be thankfull.

The Bioperl method is not working very well. Apparently some fields are not fill as it's required.

ADD REPLYlink written 3.7 years ago by Juke-342.2k
0
gravatar for Antonio R. Franco
3.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Take a look to this external resource

ADD COMMENTlink written 3.7 years ago by Antonio R. Franco4.0k
0
gravatar for Antonio R. Franco
3.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Isn't there a automatic annotation facility within NCBI ?. Take a look to this link

ADD COMMENTlink written 3.7 years ago by Antonio R. Franco4.0k

Yes there is. They are the one running it and annotate genomes by priority. Our species is not likely to meet their criteria soon ;)

ADD REPLYlink written 3.7 years ago by Eric Normandeau10k
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