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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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reverse mapping of annotations #75

Open noahaus opened 4 years ago

noahaus commented 4 years ago

Greetings,

I am trying to map annotations made by Roary (so really annotations of CDS made by prodigal, and that's why I am asking on this page) back to a gene name for use in Gene Ontology Analysis. Are you aware of any way to do this reverse mapping?

To be a bit more explicit, this is my dilemma:

group_250 |   | PE-PGRS family protein PE_PGRS17 group_345 | lipY_3 | PE-PGRS family protein PE_PGRS16 group_494 |   | putative protein group_503 |   | Ribonuclease VapC31 group_504 |   | Ribonuclease VapC25

I'd like to take the annotation in the 3rd column and update the first column with the gene name.

Any help would be greatly appreciated. Noah A. Legall

tseemann commented 4 years ago

Roary doesn't make annotations. It just uses the ones in the GFF files you provide it. Which is usually Prokka annotations. And yes, these are prodigal for the coordinates, but not for the naming of genes.

What you are asking has nothing to do with prodigal though?

You either need to improve the annotation in the GFF file, and then manipulate the spreadsheet that roary produces?