Task Name: pfm-search
Searches for transcription factor binding sites (TFBS) with position weight matrices (PWM) converted from input position frequency matrices (PFM) 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 PFM. [String, Required]
out — output Genbank file.
name — name of the annotated regions. [String, Optional, Default: “misc_feature”]
type — type of the matrix. [Boolean, Optional, Default: false]
The following values are available:
- true (dinucleic type)
- false (mononucleic type)
Dinucleic matrices are more detailed, while mononucleic ones are more useful for small input data sets.
algo — algorithm used to convert a PFM to a PWM. [String, Optional, Default: “Berg and von Hippel”]
The following values are available:
- Berg and von Hippel
- Log-odds
- Match
- NLG
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 pfm-search --seq=in.fa --matrix=MA0265.1.pfm;MA0266.1.pfm --out=res.gb