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Creating An Rpsblast Database From An Hmm Profile Library

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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.


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