Nhmmer reports different e-values (consistently off by an exact factor of 2) when I run against a fasta and a hmmerdb made from that fasta using makehmmerdb.
Reproduction
Download rfam, let's call it rfam.fasta.
Produce HMMERDB from the downloaded fasta:
makehmmerdb rfam.fasta rfam.hmmerdb
Run Nhmmer against the hmmerdb:
nhmmer --tblout /tmp/tblout.txt --rna --watson -A /tmp/output.a3m /tmp/query.a3m rfam.hmmerdb
Run Nhmmer against the fasta:
nhmmer --tblout /tmp/tblout.txt --rna --watson -A /tmp/output.a3m /tmp/query.a3m rfam.fasta
Expected result
Since I ran with --watson, I would expect the e-values to match, but they are consistently off by a factor of 2, with the hmmerdb being 2x larger.
More observations
There are 12 cases: {watson, crick, both} × {fasta, hmmerdb} × {z-value set, z-value unset}
If I set the z-value, the e-values are consistent.
If I don't set --watson or --crick, the e-values are also consistent.
I would expect the e-values to not depend on whether I used fasta or hmmerdb.
Nhmmer reports different e-values (consistently off by an exact factor of 2) when I run against a fasta and a hmmerdb made from that fasta using
makehmmerdb
.Reproduction
Download rfam, let's call it
rfam.fasta
.Produce HMMERDB from the downloaded fasta:
Run Nhmmer against the hmmerdb:
Run Nhmmer against the fasta:
Expected result Since I ran with
--watson
, I would expect the e-values to match, but they are consistently off by a factor of 2, with the hmmerdb being 2x larger.More observations
--watson
or--crick
, the e-values are also consistent.