Question: Where is it possible to submit annotated eukaryote genomes?
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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?

ADD COMMENTlink 4.4 years ago Eric Normandeau 10k • updated 4.4 years ago Antonio R. Franco ♦ 4.0k
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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][1]. ENA => We developed [EMBLmyGFF3][2] allowing to prepare the EMBL flat file ready to submit to ENA from gff3+fasta files. [1]: https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/ [2]: https://github.com/NBISweden/EMBLmyGFF3

ADD COMMENTlink 2.1 years ago Juke-34 ♦ 2.2k
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Thank you. I contacted them to ask about the annotation format they require.

ADD REPLYlink 4.4 years ago
Eric Normandeau
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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.

https://www.biostars.org/p/155268/#155557

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 4.4 years ago
Juke-34
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Take a look to this external resource

ADD COMMENTlink 4.4 years ago Antonio R. Franco ♦ 4.0k
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Isn't there a automatic annotation facility within NCBI ?. Take a look to this link

ADD COMMENTlink 4.4 years ago Antonio R. Franco ♦ 4.0k
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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 4.4 years ago
Eric Normandeau
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