Searching for TFBS with SITECON

Task Name: sitecon-search

The tool searches for transcription factor binding sites (TFBS) using SITECON and saves the identified regions as annotations.

Parameters:

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

• inmodel — Input SITECON profile(s). If several profiles are supplied, the tool searches using all profiles one by one and outputs a merged set of annotations for each input sequence. [String, Required]

• out — Output Genbank file. [String, Required]

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

• min-score — Recognition quality threshold. The value must be between 60 and 100. Choosing a threshold too low will result in recognizing too many TFBS with low reliability, while choosing it too high may result in no TFBS being recognized. [Number, Optional, Default: 85]

• min-err1 — Setting for filtering results, minimum value of Error type I. [Number, Optional, Default: 0]

• max-err2 — Setting for filtering results, maximum value of Error type II. [Number, Optional, Default: 0.001]

• 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 sitecon-search --in=input.fa --inmodel=profile.sitecon --out=res.gb