Searching for TFBS with Weight Matrices

Task Name: pwm-search

This task searches for transcription factor binding sites (TFBS) using position weight matrices (PWM) and saves the identified regions as annotations.

Parameters:

• seq — a semicolon-separated list of input sequence files in which to search for TFBS. [String, Required]

• matrix — a semicolon-separated list of the input PWMs. [String, Required]

• out — the output Genbank file.

• name — the name of the annotated regions. [String, Optional, Default: “misc_feature”]

• min-score — the 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