Task Name: pwm-search
Searches for transcription factor binding sites (TFBS) with position weight matrices (PWM) and saves the regions found as annotations.
Parameters:
seq — semicolon-separated list of input sequence files to search TFBS in. [String, Required]
matrix — semicolon-separated list of the input PWM. [String, Required]
out — output Genbank file.
name — name of the annotated regions. [String, Optional, Default: “misc_feature”]
min-score — minimum percentage score to detect TFBS. [Number, Optional, Default: 85]
strand — strands to search in. [Number, Optional, Default: 0]
The following values are available:
- 0 (both strands)
- 1 (direct strand)
- -1 (complement strand)
Example:
ugene pwm-search --seq=input.fa --matrix=Aro80.pwm;Aft1.pwm --out=res.gb