| Bioinformatics Toolbox | |
Plot an HMM profile
showhmmprof(Model, 'PropertyName', PropertyValue...) showhmmprof(..., 'Scale', ScaleValue) showhmmprof(..., 'Order', OrderValue)
Model | Hidden Markov model created with the functions gethmmprof and pfamhmmread functions. |
| Scale | Property to select a probability scale. Enter one of the following values: 'logprob' — Log probabilities 'prob' — Probabilities 'logodds' — Log-odd ratios |
showhmmprof(Model, 'PropertyName', PropertyValue...) plots a profile hidden Markov model described by the structure Model.
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(..., '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.
load('hmm_model_examples','model_7tm_2') % load a model example
showhmmprof(model_7tm_2,'Scale','logodds')
Bioinformatics Toolbox functions gethmmprof, hmmprofalign, hmmprofestimate, hmmprofgenerate, hmmprofstruct, pfamhmmread
| | showalignment | sptread | |
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