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?
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Eric Normandeau
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.
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.
Thank you. I contacted them to ask about the annotation format they require.
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.
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 thankful.
The Bioperl method is not working very well. Apparently some fields are not fill as it's required.
Take a look to this external resource
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Antonio R. Franco
Isn't there a automatic annotation facility within NCBI? Take a look at this link.
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Antonio R. Franco
Yes there is. They are the one running it and annotate genomes by priority. Our species is not likely to meet their criteria soon ;)
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