How To Reconstruct A Consensus From A Hmmer Hmm Profile

Question

[Miguel Pignatelli]

Hi,

I am trying to (and understand how to) extract the consensus of a protein alignment from its HMM profile (produced by HMMer2). I understand that from the "match emission line" I can get the corresponding amino acid (the one with the higher match emission score) when the most probable transition is 'm->m'. Am I right in assuming that a "dot" has to be inserted in the consensus when the most probable transition is 'm->d' or 'd->d'? what happens with 'd->', 'm->i', and 'i->i'? Any help would be appreciated.

Cheers,

M;

Answer 1

[robert.d.finn]

Try using the program hmmemit from the HMMER suite. I think that you need the -c option to get the consensus... The -h will list all options.

And yes a . Represents an insert respect to the model and a dash a delete state.

Best

Rob

[Miguel Pignatelli]

hmmemit makes it. I can get all the information I need to understand the process from the source code. Thanks!