hmmer e-value

Question

[CHINMAYA]

I want to run my fasta file in hmmer against pfam database with E-value ≤ e^0.001, but there is lot of confusion in how to put E-value. I run it like

$ hmmpress Pfam-A.hmm
$ hmmscan --cpu 8 -E 0.001 -o file Pfam-A.hmm mix.fa

and what are the meaning of these

 -E <x>     : report models <= this E-value threshold in output  [10.0]  (x>0)
 -T <x>     : report models >= this score threshold in output
 --domE <x> : report domains <= this E-value threshold in output  [10.0]  (x>0)
 --domT <x> : report domains >= this score cutoff in output

and how to use these options?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[CHINMAYA]

ok thank you

Answer 1

[Mensur Dlakic]

The way you typed the command is correct. You may want to add --tblout file.tbl to also save the results as a table.

Score thresholds will use scores recorded in HMMs instead of E-values. It is one of those expert options that is difficult to generalize for the whole database, as they are intended to catch borderline true positives. Use it only if you know what you are doing.