Exact match with query architecture option for local version of HMMER

Question

[Sej Modha]

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?

Answer 1

[Sej Modha]

I have concluded that this is feature is not available in the current version of the local HMMER tool.

[Allen]

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.