| Bioinformatics Toolbox | |
Generate a random sequence drawn from the profile HMM
Sequence = hmmprofgenerate(Model,
'PropertyName', PropertyValue....)
[Sequence, Profptr] = hmmprofgenerage(Model)
hmmprofgenerate(..., 'Align', AlignValue)
hmmprofgenerate(..., 'Flanks', FlanksValue)
hmmprofgenerate(..., 'Signature', SignatureValue)
| Model | Hidden Markov model created with the function hmmprofstruc. |
| Align | Property to control using upper case letters for matches and lower case letters for inserted letters. Enter either true or false. The default value is false. |
| Flanks | Property to control including the symbols generated by the FLANKING INSERT states in the output sequence. Enter either true or false. The default values is false. |
| Signature | Property to control returning the most likely path and symbols. Enter either true or false. Default value is false. |
Seq = hmmprofgenerate(Model, 'PropertyName', PropertyValue...) returns a string (Seq) showing a sequence of amino acids or nucleotides drawn from the profile (Model). The length, alphabet, and probabilities of the Model are stored in a structure. For move information about this structure, see hmmprofstruct).
[Sequence, Profptr] = hmmprofgenerage(Model) returns a vector of the same length as the profile model pointing to the respective states in the output sequence. Null pointers (0) mean that such states do not exist in the output sequence, either because they are never touched (i.e. jumps from the BEGIN state to MATCH states or from MATCH states to the END state), or because DELETE states are not in the output sequence (not aligned output; see below).
hmmprofgenerate(..., 'Align', AlignValue) if Align is true, the output sequence is aligned to the model as follows: uppercase letters and dashes correspond to MATCH and DELETE states respectively (the combined count is equal to the number of states in the model). Lowercase letters are emitted by the INSERT or FLANKING INSERT states. If Align is false, the output is a sequence of uppercase symbols. The default value is true.
hmmprofgenerate(..., 'Flanks', FlanksValue) if Flanks is true, the output sequence includes the symbols generated by the FLANKING INSERT states. The default value is false.
hmmprofgenerate(..., 'Signature', SignatureValue) if Signature is true, returns the most likely path and symbols. The default value is false.
load('hmm_model_examples','model_7tm_2') % load a model example
rand_sequence = hmmprofgenerate(model_7tm_2)
Bioinformatics Toolbox functions hmmprofalign, hmmprofstruct, showhmmprof
| | hmmprofestimate | hmmprofmerge | |
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