How Do I Convert A Log-Likelihood Obtained From Hmmer To An E-Value Or Vice-Versa?

Question

[arronslacey]

Hi - I have created a hmm profile for some transport proteins using hmmer, and used the hmmsearch function to return the e-value of the query sequence. I have also built a hmm model using the bayesian network tool in matlab - where the output is in the form of a log-likelihood. My question is how do I convert a log-likelihood to an e-value or vice-versa.

Thanks very much,

Arron.

[Fabio Marroni]

I am not expert in protein structure, but are you sure you don't have to use hmmsearch on the hmm model obtained in matlab? Looks like in the first step you built a protein profile and then searched it against a database (which returns E-value) and in the second you created a protein model (for which you obtained confidence in the form of log-likelihood), but to compare with the first profile I think you still need to perform a search against the very same database.