Closed ZhangDengwei closed 1 year ago
You're looking at a per-sequence tabular output. All these sequences have passed the per-sequence bitscore thresholds you set (-T
and --incT
).
Look at the --domtblout
domain output, per-domain, and you'll see that none of the domains from these sequences have been reported or considered significant, because of your reporting (--domT
) and inclusion (--incdomT
) thresholds.
HMMER distinguishes between the score and significance of whole sequences vs. individual domains.
Thanks for the interpretation. I still have a doubt about the hit inclusion in the first round when using the aforementioned command. I still found that some hits with domain bitscore < 20 were considered significant in the 1st iteration and used for the next round of searching. Did I misunderstand the output of out.jackhmmer_B20
?
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
+ 4.2e-05 37.1 33.0 2.3e+05 6.5 0.1 12.7 0 UniRef100_UPI001EE5AE5F uncharacterized protein LOC124274692
Same answer. That line is telling you about a sequence, not an individual domain. If you want to see which domains were flagged for inclusion, look at the domain section of the main output, or use --domtblout
for tabular output.
See the User Guide for more information.
Hi,
I am using
jackhmmer
to iteratively search my query sequences against UniRef100, with the command as follows:jackhmmer -N 5 -o parameter_examination/out.jackhmmer_B20 -A parameter_examination/out.MSA_B20 --tblout parameter_examination/out.seq.tblout_B20 -T 20 --domT 20 --incT 20 --incdomT 20 --cpu 20 query.fa uniref100.fasta
I want to control the hit with domain bitscore > 20 instead of sequence bitscore > 20, but I found some significant hits have a sequence bitscore > 20 but domain score < 20, for example,
Even though I only set
--incT 20
with missing--incdomT 20
, the output did not change. Is there any problem with my command? How can I control the hit according to domain's bitscore rather than sequence's bitscore? Any suggestions provided would be much appreciated!