Creating An Rpsblast Database From An Hmm Profile Library

Question

[Michael Schubert]

I have downloaded the HMM library file from CATH and would like to convert it to a rpsblast database.

Therefor, I think I need to do the following steps:

1. Extract the HMM profiles from the library (this seems to be a simple split at //)
2. Convert each profile into a PSSM (with something like this)
3. 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.

Answer 1

[Neilfws]

Your approach sounds reasonable. Another solution is outlined in this HMMER tutorial - scroll down to "Using an HMM model to create an alignment". It is for HMMER 2.3.2; I don't know if CATH has moved to HMMER3 to build profiles?

Basically, they suggest using hmmalign on a set of sequences retrieved from hmmsearch. The resulting alignment can then be used to build a PSSM. However, your solution might be quicker, if you can go straight from HMMER profile to PSSM.