Maker yields sequences without start and stop codon

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Maker yields sequences without start and stop codon

Emmanuel Nnadi
I ran my annotation using ESTs from NCBI and transcriptome data and Swiss-prot data. I used SNAP trained twice after which Augustus was trained once.

I tried to submit the annotated genome to NCBI but have some problems I have not experienced before and do not know how to solve.

Some of the CDS features have invalid translations. Every CDS feature should have a valid start and stop codon, and should not have any internal stops.  The only exception is if the CDS is partial at the end of a sequence or at an intron/exon boundary.  If the CDS is partial, it must have the appropriate partial symbols.  

If a CDS feature does not have a valid translation (for example if there is a frameshift), please remove the CDS feature and annotate this with a single gene feature across the entire span.  Include a note on the gene with a brief description.  For example:

1       200     gene
                        gene    phoA
                        gene_desc       alkaline phosphatase
                        locus_tag     OBB_0001
                        note    nonfunctional due to frameshift

[3] There are 1075 gene features that are not associated with
any other features (CDS, rRNA, etc.) and are not labelled as
pseudogenes or as nonfunctional genes.  Did you lose some of
the annotation you intended to include.

Please how can this be solved?


Nnadi Nnaemeka Emmanuel,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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