This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Creating An Rpsblast Database From An Hmm Profile Library

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.

hmmer blast conversion
• 3,948 views • link
updated by Neilfws Neilfws • written by Michael Schubert Michael Schubert

1 answer

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.

• 2 views • link
written by Neilfws Neilfws

Log in to answer this question.

More posts like this