Hi mates, I was reading a paper which it states they identify protein sequences in Halyomorpha halys genome performing a local BLASTp search using the PFAM domain (PF00112) as query (paper) It is driving me mad because I couldn't do it. The main doubt I have is how can I be able to add a PFAM domain as query in a BLASTp? is it that possible? Because PFAM domains are HMM and not a unique sequence.
The main idea behind it is to search for papain family cysteine protease domains in the proteome of Halyomorpha halys
Thanks in advance,
Thanks a lot Mensur! That's what I was looking for! I'm gonna try that package and see how it goes! Now it is clearer, it's logical to use a consensus sequence which comes from a HMM file!
Regards. Gerardo