Nowadays, I am trying to work on finding the protein domains by using hmmscan (HMMER 3.2.1).
So, I have a file that multiple protein sequences exist and downloaded Pfam.A.hmm and this file.
Then I followed the "User's Guide" of Hmmer which was released on here to install it properly.
Here are my steps after installation:
hmmbuild Pfam-A.hmm Pfam-A.seed hmmpress Pfam-A.hmm hmmscan <my_sequence_file> Pfam-A.hmm
Could you inform me if I made mistake so far, please?
Then, I got these results:
Now, I couldn't find a proper values to filter them and configure the threshold. At this point, I tried some values as a threshold for both e-value and score but the results were not satisfactory.
Actually, I'm wondering that what kind of elimination was used on Hmmscan online service. Even though I read some pages such as Hmmer web services docs and here to filter and determine a threshold, I couldn't understand what I should do.
I will be waiting your replies.
Thanks in advance...