Searching HMM Signals Using HMMER2

Task Name: hmm2-search

This task searches each input sequence for significantly similar sequences that match all specified profile HMMs using the HMMER2 tool.

Parameters:

• seq: A semicolon-separated list of the input sequence files. [String, Required]

• hmm: A semicolon-separated list of the input HMM files. [String, Required]

• out: The output file with annotations. [String, Required]

• name: The name of the result annotations. [String, Optional, Default: “hmm_signal”]

• e-val: The e-value 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:

ugene hmm2-search --seq=CBS_seq.fa --hmm=CBS.hmm --out=CBS_hmm.gb