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Searches a sequence for significantly similar sequence matches with one or more profile HMM and saves the results as annotations.

The search is performed using HMMER3 hmmsearch tool integrated into UGENE.

Parameters in GUI

General parameters:

ParameterDescriptionDefault value
Annotate AsName of the result annotations.hmm_signal
Profile HMMSemicolon-separated list of input HMM files.You must specify a value!
Min LengthMinimum length of a result region.30
Max LengthMaximum length of a result region.5000


Parameters controlling reporting threshold:

Reporting thresholds controls which hits are reported.

ParameterDescriptionDefault value
Use E-valueFilter by E-value if true. Otherwise, filters by score.True
Filter by High E-valueReports domains <= this E-value threshold in output (hmmsearch–domE option).1e+1
Filter by Low ScoreReports domains >= this score cutoff in output (hmmsearch–domT option).0.01


Parameters controlling the acceleration pipeline:

HMMER3 searches are accelerated in a three-step filter pipeline: the MSV filter, the Viterbi filter, and the Forward filter. The first filter is the fastest and most approximate; the last is the full Forward scoring algorithm. There is also a bias filter step between MSV and Viterbi.

ParameterDescriptionDefault value
MaxTurns off all acceleration heuristic filters. This increases sensitivity somewhat, at a large cost in speed.False
MSV Filter ThresholdP-value threshold for the MSV filter step.0.02
Viterbi Filter ThresholdP-value threshold for the Viterbi filter step.0.001
Forward Filter ThresholdP-value threshold for the Forward filter step.1e-5
No Bias FilterTurns off composition bias filter. This increases sensitivity somewhat, but can come at a high cost in speed.False


Other parameters:

ParameterDescriptionDefault value
No Null2Turns off the null2 score corrections for biased composition.False
Number of SequencesSpecifies number of significant sequences. It is used for domain E-value calculations (hmmsearch–domZ option).1 (i.e. one input sequence)
SeedRandom number seed. The default is to use a fixed seed(42), so that results are exactly reproducible. Any other positive integer will give different (but also reproducible) results. A choice of 0 uses a randomly chosen seed.42


Parameters in Schema File

Type: hmm3

ParameterParameter in the GUIType
keyAnnotate Asstring
min-lenMin Lengthstring
max-lenMax Lengthstring
hmm-profileProfile HMMstring
use-e-valUse E-valueboolean
e-valFilter by High E-valuenumeric
scoreFilter by Low Scorenumeric
msv-filter-thresholdMSV Filter Thresholdnumeric
viterbi-filter-thresholdViterbi Filter Thresholdnumeric
forward-filter-thresholdForward Filter Thresholdnumeric
no-bias-filterNo Bias Filterboolean
no-score-correctionsNo Null2boolean
seqs-numNumber of Sequencesnumeric
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