With Wormmart I was relatively easily able to get all Hawaiian SNPs from a specified interval that resulted in missense, nonsense or indel mutations in the corresponding proteins.
I’ve almost figured out how to get the Hawaiian SNPs in a region using Wormmine, but can I then filter or sort them based on the molecular effects? Or if anyone knows of another way to get this information, that would be great too.
Thanks!
Personally, I would have extracted the snps and their consequences from the GFF2/3 files.
But if you could share how you got them out of WormMine, maybe we can help.
With WormMine the filters were in the Variation data set:
[ol]- [General] Variation Type that were Predicted_SNP’s
- [Molecular] Effect on protein that was nonsense/missense etc
- Location specified
- [Isolation] strain CB4856[/ol]
And the Attributes output was:
[ol]- Affects Gene, select [Molecular] Gene Info (merged)
- Protein Change (nonsense/missesnse etc)[/ol]