[maker-devel] Error trying to submit genome to ncbi

[Daniel Ence]

Hi, I think you’ve posted before about issues 1 and 2 from the NCBI. The note for issue 3 from NCBI sounds like there are gene features that don’t have associated transcript, CDS or exon features. I’m not certain how that could be a result from MAKER. It might be something that someone else created (manually or with another tool), and then passed to maker from a GFF file. In the example included in your email, it looks like these offending genes are transposons that have been annotated as genes. If that is the case for the rest of the offending genes, then I would suggest changing the “type” field (column 3) from “gene” to something else, like “transposable_element” perhaps. 

~Daniel


> On Nov 2, 2017, at 3:51 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hi,
> 
> I am trying to submit my genome i annotated using maker and they sent back this error,
> 1. Please remove any N nucleotides from the beginning or end of the sequence
>  2.No feature should begin or end inside a gap.  Instead the feature should
> be made partial at the gap boundary.
> 
> [3] Coding regions should not be 5' partial if they begin with the start
> methionine.  If this is an internal methionine int he translation than
> it is fine if they are partial.  Conversely, all coding regions
> must have a stop codon or be 3' partial.
> You have a large number of gene features that are not associated
> with other features.  Please include on these features in the
> gene description field some description of what the gene would
> have encoded.
> 
> A feature table example of this is:
> 
> <41156  >40652  gene
>                         gene_desc       transposon
>                         locus_tag       CR513_45338
>                         note    nonfunctional due to frameshift
> Please how can i use maker to solve this problem?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://www.researchgate.net/profile/Emmanuel_Nnadi/publications>_______________________________________________
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