I am using hmmbuild to build a HMM with 89 domains, and searching all arabidopsis proteins against the 89 domains using hmmsearch :
hmmsearch -Z 2000000 --domZ 89 --cpu 20 -o output.hmmsearch.txt stockholm89.hmm at_pep
It just cost less than 2 minutes to finish the search.
To speed this search, only 1300 interesting proteins were selected to perform the searching using the same command. But it takes about 20minutes.
I use the latest version of HMMER. Does any known the problem about it? Is it a bug for the hmmsearch program?