read a Dirichlet prior to replace default mixture Dirichlet in Hmmer-3.2.1

[qianfeng2]

Dear whom it may concern,

I hope you are well:)

I notice that default mixture Dirichlet prior parameters for protein models are built in when I am using hmmbuild command of Hmmer-3.2.1. Is it possible to change this built in prior when implementing hmmer3, since I am doing research about the impact of hidden states' transition priors? If so, how to do it?

Specifically, I only want to change the numbers among transition parameters, for instance, change the M-D alpha from 0.0135 to 0.0278, change M-I alpha from 0.0278 to 0.0135.

Admittedly, I know hmmer-2.3.2 can achieve this by reading a prior to replace the default Dirichlet prior. We believe continue to using hmmer3 is our best choice.

Any comment is much appreciated!

Best regards, Qian

[cryptogenomicon]

You're correct, HMMER3 hmmbuild doesn't have an option for reading in a customized prior.

To change the prior, you can edit the built-in prior in src/p7_prior.c, for example editing the function p7_prior_CreateAmino() to change the protein model prior.

[qianfeng2]

Great! It works now!

Thank you very much @cryptogenomicon