[maker-devel] NCBI feature table

[Brian Hall]

Hi Ian,

My colleagues are also working on preparing a genome for submission to 
the NCBI. The software we are developing for this task is still a work 
in progress, but you are welcome to give it a try:

https://github.com/tedsta/GAG

It's a console-based application and it requires Python 2.6. Its 
strength is in filtering and modifying large segments of the genome at 
once -- where Apollo is good for removing a few erroneous exons, we are 
dealing with lists of dozens or more. This program seeks to make such 
changes as painless as possible.

My advice is to try the simplest gff3-to-tbl script you can find and 
then run tbl2asn. If it works out okay, great! If you get a massive 
error report, get in touch and we'll help you out if we can :)

--Brian

On 02/07/2014 05:16 AM, maker-devel-request at yandell-lab.org wrote:
> Date: Fri, 7 Feb 2014 08:29:27 -0500
> From: UMD Bioinformatics <bioinformatics.umd at gmail.com>
> To: maker-devel at yandell-lab.org
> Subject: [maker-devel] NCBI feature table
> Message-ID: <22EBA1A9-1DE2-4898-8010-4856E67F3AF8 at gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Hello Maker Developers,
>
> I have used this software with great success and I continue to look to it going forward. However, as I?m getting ready to submit my annotations to NCBI with the genomes I haven?t found a straightforward method of turning the MAKER produced GFF files into a NCBI feature table. What is the process for creating this table? It seem that the format NCBI is looking for is unique and I haven?t uncovered any scripts or tools to assist in the creation of this table from my annotation files. If anyone has any insight on this issue it would be greatly appreciated.
>
> Cheers
> Ian
>