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HMMER tool in more details

Official HMMER User's Guide
http://eddylab.org/software/hmmer/Userguide.pdf

Brivez run hmmsearch as the following:
hmmsearch --domtblout table.output -E 1e-5 --domE 1e-5 --cpu 2 hmmfile target.fastsa

This line can be edited at line 95 inside brivez_man.sh.

-E 1e-5
Report target sequences with an E-value of <= X. The default is 10.0 (read p. 104).
--domE 1e-5
For target sequences that have already satisfied the per-profile reporting threshold, report individual domains with a conditional E-value of <= X. The default is 10.0 (read p. 104).
--cpu 6
Set the number of parallel worker threads to N. On multicore machines, the defaults is two. Can be use also --mpi in alternative (read p. 107).

From the table.output are extracted two kind of coordinates:

ali coord
The start of the MEA alignment of this domain with respect to the sequence (read p. 72)
env coord
The start and the end of the domain envelope on the sequence. (read p. 72)

By default, Brivez use the env coord, but it's possible to change it on line 43 in ./00_script/brivez_script02.py:

change df_selected = df[["target_name", "query_name", "accession1", "START_ali", "END_ali"]]
with df_selected = df[["target_name", "query_name", "accession1", "START_envelope", "END_envelope"]]

Useful things to know:

hmmpress is useful only if used with hmmscan (read p. 97)
MEA Maximum Expected Accuracy
envelope When HMMER identifies domains, it identifies what it calls an envelope bounding where the domain’s alignment most probably lies. The envelope is almost always a little wider than what HMMER chooses to show as a reasonably confident alignment.