Building PWM

Task Name: pwm-build

This task builds a position weight matrix (PWM) from a multiple sequence alignment (MSA) file.

Parameters:

• in — a semicolon-separated list of input MSA files. [String, Required]

• out — the output file. [String, Required]

• 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 — the algorithm used to build the matrix. [String, Optional, Default: “Berg and von Hippel”]

  The available options are:

  • Berg and von Hippel
  • Log-odds
  • Match
  • NLG

Example:

ugene pwm-build --in=COI.aln --out=result.pwm