Set a %coverage threshold during a hmmsearch using HMMer

Hi everyone,

I would like to know if there is a way to set a %coverage treshold using hmmsearch. I’ve read the user guide, but i haven’t found it.

Regards,

C.

You’ll need to provide a definition of “%coverage” to be sure, but the answer is almost certainly “no”. 

When I hear “%coverage”, I think of a measure of shared length, probably “what percent of the sequence is aligned to the model” (or vice versa).  If this is what you’re after, you may want to use hmmsearch’s –tblout flag. This will give you an easy-to-parse space-delimited file that includes start/end-positions for both the query model and the target sequence, along with the total target sequence length. Knowing the model length also, the %coverage math from there is pretty easy to pull off.