I have recently realized that hh-suite has removed support for HMMER files completely. I was wondering if there was a utility to convert HMMER format to the new HHSearch format, or even some kind of guide to explain what the differences are so that I could implement it myself.
Regenerating the profiles is not possible, since the profile itself is the output of my program, not an alignment.
One (horrible) hack for things to work for the moment has been to use hmmemit and generate a few sequences, align them using hmmalign, then feed this to hmmake to create an .hhm file, and then send that to hhblits. This works, but there must be a much much better way.
jamaliki
commented
1 year ago
I have recently realized that hh-suite has removed support for HMMER files completely. I was wondering if there was a utility to convert HMMER format to the new HHSearch format, or even some kind of guide to explain what the differences are so that I could implement it myself.
Regenerating the profiles is not possible, since the profile itself is the output of my program, not an alignment.
One (horrible) hack for things to work for the moment has been to use hmmemit and generate a few sequences, align them using hmmalign, then feed this to hmmake to create an .hhm file, and then send that to hhblits. This works, but there must be a much much better way.