hmmprofgenerate
Generate random sequence drawn from profile hidden Markov model (HMM)
Syntax
Sequence = hmmprofgenerate(Model)
[Sequence, Profptr]
= hmmprofgenerate(Model)
... = hmmprofgenerate(Model, ...'Align', AlignValue, ...)
... = hmmprofgenerate(Model, ...'Flanks', FlanksValue, ...)
... = hmmprofgenerate(Model, ...'Signature', SignatureValue, ...)
Arguments
Model | Hidden Markov model created with the |
AlignValue | Controls the use of uppercase letters for matches and
lowercase letters for inserted letters. Choices are |
FlanksValue | Controls the inclusion of the symbols generated by the
FLANKING INSERT states in the output sequence. Choices are |
SignatureValue | Controls the return of the most likely path and symbols.
Choices are |
Description
Sequence = hmmprofgenerate(Model)Model.
The length, alphabet, and probabilities of the Model are
stored in a structure. For more information about this structure,
see hmmprofstruct.
[ 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).Sequence, Profptr]
= hmmprofgenerate(Model)
... = hmmprofgenerate( calls Model, ...'PropertyName', PropertyValue, ...)hmmprofgenerate 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 quotes and is case insensitive. These property
name/property value pairs are as follows:
... = hmmprofgenerate( if Model, ...'Align', AlignValue, ...)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 AlignValue is false,
the output is a sequence of uppercase symbols. The default value is true.
... = hmmprofgenerate( if Model, ...'Flanks', FlanksValue, ...)Flanks is true,
the output sequence includes the symbols generated by the FLANKING
INSERT states. The default value is false.
... = hmmprofgenerate( if Model, ...'Signature', SignatureValue, ...)SignatureValue is true,
returns the most likely path and symbols. The default value is false.
Examples
load('hmm_model_examples','model_7tm_2') % load a model example
rand_sequence = hmmprofgenerate(model_7tm_2)
Version History
Introduced before R2006a
