HMM-HMM comparison - beginner

[lalalagartija]

Hi,

where can I find documentation to create a custom hmm database ?

For the moment I have done a database starting with msa. I followed your exact tutorial except for the secondary structure prediction because I have not installed hhpred.
I then use hhsearch or hhblits to search this hmm database starting with an msa or hmm as query :
hhsearch -i HMMs/${i}.hhm -d ${db} -E 0.01 -blasttab tmpHMMsearch
In the output I get a line for each sequence in the database it matched. I was expecting a comparison to the overall alignment. Should I start by constructing a concensus sequence database ?

Thanks very much in advance