figures are wrong when ips run with proteins instead of mRNA

[bradfordcondon]

We run iPS on the polypeptides and then run the loader, linking to the parent mRNA.

However, the resulting plot gets messed up. The alignment is relative to the protein, but the full drawing is relative to the mRNA. We do not have entity pages for proteins, just mRNA. So the drawing everything gets squished into the first 1/3 of the mRNA because thats the corresponding protein....

Whats the right way to solve this?

Option in field to "transpose" alignment coordinates?
Auto transpose is fieldd is attached to mRNA instead of protein?
Some smarter way of tracking the coordinates?
Draw the figure relative to the protein positions instead (IE get the length from the related polypeptide)?

[kyrenya]

Hi! I take advantage of this thread because I'm a bit confused with the correct use of the interpro module:

I have already publish genes and mRNAs

I'm following the documentation for functional modules, and I read that in the citrus example, apparently the interpro .xml is obtained from mRNAs..

My interpro analysis is done from the GCF_######.protein.faa file:
I created an interpro analysis, and chose the following parameters, hoping (dont know if its the best approach) the module to find the proteins in the features of the database uploaded with the gff:

Query: CDS

Am I doing fine?

Thanks in advance :)

[kyrenya]

ok, so I made a little test with only one sequence query, and the file uploads, but doesnt match with anything, apparently. I throw here a bunch of questions to see if I understand how this should work :)

1st. The citrus example is done from a mRNA file? Why?

2. If I have run interproscan for a proteins file, can I link it to my mRNA/genes entries? or I'm supposed to have proteins entries in my site or sth like that?

3. If my interpro xml file looks like this.....
   

I am supposing that I have to link the "XP_########" to my features in my database, but don't know how..

I appreciate any shed of light here.
Thanks

[bradfordcondon]

1st. The citrus example is done from a mRNA file? Why?

Because we want the annotations to display on the MRNA entity page, not a protein entity page. Thats why it uses the mrna as the query.

If I have run interproscan for a proteins file, can I link it to my mRNA/genes entries? or I'm supposed to have proteins entries in my site or sth like that?

you can link it to the mrna. You need to specify the Query Type as mRNA, and provide a regular epxression if necessary.

I am supposing that I have to link the "XP_########" to my features in my database, but don't know how..

yep. So you ned a regular expression that will link XP_### to the mRNA name. If thats not possible, then you'll have to link the interproscan results to the protein and display it there, until we implement a better way.

edit: if you have further questions, please create a unique issue. this issue is for discussing a specific problem with linking interproscan queries run on proteins to mRNA.

[kyrenya]

ok! I will work on this and open other issue if I dont manage!
Thanks a million!