Opened 22 hours ago

Last modified 22 hours ago

#20191 assigned enhancement

Extract allele frequency from fetched uniprot variants info

Reported by: Tom Goddard Owned by: Tom Goddard
Priority: moderate Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Would be interesting to see allele frequency and minor allele frequency in fetched uniprot variants data. These can be two more scores in addition to the polyphen2 and sift pathogenicity scores.

Change History (1)

comment:1 by Tom Goddard, 22 hours ago

Done.

Trying to display allele frequency for opioid receptor P35372 together with pathogenicity data on one heatmap revealed problems. The heatmap uses the same colormap for each score and the frequency data wants colors blue, white, red around 1e-5, 1e-4, 1e-3 while the pathogenicity wants 0, .5, 1.

Another heatmap problem was that allele frequency was not available for some residues where pathogenicity was (e.g. 1-4) and showing allele frequency caused the heatmap to omit those residues.

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