Hello Biostars,
I am trying to search a customised HMM profile against the refseq protein databases using hmmsearch (HMMER 3.1b1) locally on my computer. I have performed a similar search against the UniProt DB available on https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch. The online version of the HMMER allows me to filter the sequences that match the exact query architecture, however, I am unable to find a similar option that allows me to filter the results obtained with local hmmsearch.
Is it possible to filter results that match exact query architecture in the local hmmsearch?
Hello, Sej! I've met the same problem with you. I try to do the hmmscan for all full-length of the target sequences given by phmmer, and then check whether their full-length sequences contain exactly the same domain as the query sequence does. But it turns out the result I get is different from the exact match from the online service. So, have you solved the problem? Maybe you can give me a hint.