Forum:Clustering proteins by Pfam annotation

Question

[konstantinkul]

Hi all,

What do you think is it possible to cluster annotated proteins (using InterProScan) by (for example) Pfam IDs? The issue is that each protein may have several Pfam IDs (several domains, families etc). This is just an idea of clustering by functional annotation, I tried Orthotomcl, Spectral Clustering but there are many false positive and false negative matches between AA sequences.

Thank you in advance.