Therefor, I think I need to do the following steps:
- Extract the HMM profiles from the library (this seems to be a simple split at //)
- Convert each profile into a PSSM (with something like this)
- Use formatrpsdb to create a database from the PSSMs
Is there a smarter way to do is? I do not want to use hmmsearch directly because I would like to integrate the CATHdb into an already exisiting rpsblast framework.