Automatically retrieving interpro domain information ( to combine with phylogentic tree) - PhyloXML

Question

[VenGeno]

Hi , I want to generate phylogentic tree containing interpro domains next to each gene label. I used DoMosaics but the tool earlier and now its gone for good. I found that forester and Phy3d tools are ideal for my purpose. However, I am yet to find a tool that can bulk retrieve interpro domain for each of sequence and integrate both domain info and phylogentic tree. Can someone help me on this regard. Thank you

Answer 1

[Damianos P. Melidis]

Hi Venurah,

By my little experience with Interpro database. You can retrieve for each interpro id the connecting database ids (for example PFAM, CDD, etc). Then you can check each connecting database if it contains the domain profile (multiple sequence alignment (MSA)). Then you can build the phylogenetic tree of interpro ids based on the MSAs. I am not aware of a BioPython tool that does that automatically though.

Good luck!

Damianos