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Plot hidden Markov model (HMM) profile


showhmmprof(Model, ...'Scale', ScaleValue, ...)
showhmmprof(Model, ...'Order', OrderValue, ...)


ModelHidden Markov model created by the function gethmmprof or pfamhmmread.
ScaleValueProperty to select a probability scale. Enter one of the following values:
  • 'logprob' — Log probabilities

  • 'prob' — Probabilities

  • 'logodds' — Log-odd ratios

OrderValueProperty to specify the order of the amino acid alphabet. Enter a character vector with the 20 standard amino acids characters A R N D C Q E G H I L K M F P S T W Y V. The ambiguous characters B Z X are not allowed.


showhmmprof(Model) plots a profile hidden Markov model described by the structure Model.

showhmmprof(..., 'PropertyName', PropertyValue, ...) calls showhmmprof with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

showhmmprof(Model, ...'Scale', ScaleValue, ...) specifies the scale to use. If log probabilities (ScaleValue='logprob'), probabilities (ScaleValue='prob'), or log-odd ratios (ScaleValue='logodds'). To compute the log-odd ratios, the null model probabilities are used for symbol emission and equally distributed transitions are used for the null transition probabilities. The default ScaleValue is 'logprob'.

showhmmprof(Model, ...'Order', OrderValue, ...) specifies the order in which the symbols are arranged along the vertical axis. This option allows you reorder the alphabet and group the symbols according to their properties.


  1. Load a model example.

    model = pfamhmmread('');
  2. Plot the profile.

    showhmmprof(model, 'Scale', 'logodds')

  3. Order the alphabet by hydrophobicity.

    hydrophobic = 'IVLFCMAGTSWYPHNDQEKR';
  4. Plot the profile.

    showhmmprof(model, 'Order', hydrophobic)

Introduced before R2006a

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