The Profile Comparer (PRC,
Martin Madera) is a program for aligning and scoring profile
hidden Markov models.
Here, you can input your query alignment and run PRC against profile HMM libraries of domain databases.
Your input alignment can be in
or GCG MSF format.
Using webPRC you can identify and evaluate similar alignments in Pfam,
CATH, NCBI's Conserved Domain Database (CDD)
both in HMM and alignment space.
Additionally, you can produce logos, and view or download the multiple sequence alignments corresponding to the hits.
Documentation: introduction to the PRC web server, including
You can also rerun the example.