Generate PSSM using HMMER

Question

[Tze Jet]

Is there a way to generate PSSMs using HMMER, in similar fashion as to how PSI-BLAST does it?

Answer 1

[Mensur Dlakic]

I partially answered this question in your earlier post.

The conversion you ask about involves a significant loss of information, so it is unlikely that anyone has developed a tool for it. First, a loss of precision as PSSM uses only integers. Second, there is no probabilistic treatment of indels in PSSM like in HMMs.

If you still want to pursue this, my suggestion is to do it through alignments. There is a script reformat.pl in HHsuite scripts directory that will convert between various alignment formats. Let's say you download an alignment that was used to build one of Pfam's HMMs and convert it into psiblast format. Then you can run a single search round of psiblast and ask it to save the result as a PSSM.

A more difficult way (yet more accurate) would be to extract residue frequencies from HMMs and convert them to PSSMs. This is the same in spirit as what I already explained to you about HHMs but you would have to read up about the HMMer file format and how it stores residue frequencies. HHMs (HHsuite) do not store pseudo-counts while HMMs (HHMer) do, so that makes a HMM->PSSM conversion somewhat easier.