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joiningdata / lollipops

Lollipop-style mutation diagrams for annotating genetic variations.
GNU General Public License v3.0
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Custom domain #6

Closed jhchung closed 8 years ago

jhchung commented 9 years ago

Hi,

You've got an interesting tool here. I'm testing it out but have come accross an issue with the annotations.

For one of the proteins that I am interested in, the annotations from pfam are different from other published sources including uniprot and published articles. Is there a way to add custom domain annotations? For example, to use a tab delimited text file describing the different domains as an input?

Thanks, -Jonathan

pbnjay commented 9 years ago

Does the -U option to provide uniprot ID give the wrong domain info also? I find it strange that pfam would be significantly different from uniprot.

Jeremy

On Tue, Feb 3, 2015 at 10:28 AM, jhchung notifications@github.com wrote:

Hi,

You've got an interesting tool here. I'm testing it out but have come accross an issue with the annotations.

For one of the proteins that I am interested in, the annotations from pfam are different from other published sources including uniprot and published articles. Is there a way to add custom domain annotations? For example, to use a tab delimited text file describing the different domains as an input?

Thanks, -Jonathan

— Reply to this email directly or view it on GitHub https://github.com/pbnjay/lollipops/issues/6.

jhchung commented 9 years ago

The protein I am looking at is RIPPLY3. I used -U P57055 and had no trouble getting the annotations from pfam.

In uniprot, there are two domains (Ripply and WRPW) but in pfam, there is only a Ripply domain with some disordered or low complexity domains but no WRPW domain. Also, the start and stop positions of the ripply domain is very different in the two databases.

It is strange and I don't think it's a problem with the program itself.