Task Name: hmm2-search
Searches each input sequence for the significantly similar sequence that matches to all specified profile HMM using the HMMER2 tool.
Parameters:
seq — semicolon-separated list of the input sequence files. [String, Required]
hmm — semicolon-separated list of the input HMM files. [String, Required]
out — output file with annotations. [String, Required]
name — name of the result annotations. [String, Optional, Default: “hmm_signal”]
e-val — e-value that can be used to exclude low-probability hits from the result. [Number, Optional, Default: 1e-1]
score — score based filtering which is an alternative to e-value filtering to exclude low-probability hits from the result. [Number, Optional, Default: -1000000000]
Example:
| Code Block |
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ugene hmm2-search --seq=CBS_seq.fa --hmm=CBS.hmm --out=CBS_hmm.gb |