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Searches HMM signals in a sequence with one or more profile HMM2 and saves the results as annotations.

Parameters in GUI

ParameterDescriptionDefault value
Profile HMMSemicolon-separated list of input HMM files.You must specify a value!
Min LengthMinimum length of a result region.10
Max LengthMaximum length of a result region.1000
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
Number of SequencesSpecifies number of significant sequences. It is used for domain E-value calculations (hmmsearch–domZ option).1 (i.e. one input sequence)

 

Parameters in Schema File

Type: hmm2

ParameterParameter in the GUIType
min-lenMin Lengthstring
max-lenMax Lengthstring
hmm-profileProfile HMMstring
e-valFilter by High E-valuenumeric
scoreFilter by Low Scorenumeric
seqs-numNumber of Sequencesnumeric
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