Bioinformatics Toolbox™

hmmprofalign

Align query sequence to profile using hidden Markov model alignment

Syntax

Alignment = hmmprofalign(Model,Seq)
[Alignment, Score] = hmmprofalign(Model,Seq)
[Score, Alignment, Prointer] = hmmprofalign(Model,Seq)

hmmprofalign(..., 'PropertyName', PropertyValue,...)
hmmprofalign(..., 'ShowScore', ShowScoreValue)
hmmprofalign(..., 'Flanks', FlanksValue)
hmmprofalign(..., 'ScoreFlanks', ScoreFlanksValue)
hmmprofalign(..., 'ScoreNullTransitions', ScoreNullTransitionValue)

Arguments

Description

Alignment = hmmprofalign(Model,Seq) returns the score for the optimal alignment of the query amino acid or nucleotide sequence (Seq) to the profile hidden Markov model (Model). Scores are computed using log-odd ratios for emission probabilities and log probabilities for state transitions.

[Alignment, Score] = hmmprofalign(Model,Seq) returns a string showing the optimal profile alignment.

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 states. For more information about the HMM profile, see hmmprofstruct.

[Score, Alignment, Prointer] = hmmprofalign(Model,Seq) returns a vector of the same length as the profile model with indices pointing to the respective symbols of the query sequence. Null pointers (NaN) mean that such states did not emit a symbol in the aligned sequence because they represent model jumps from the BEGIN state of a MATCH state, model jumps from the from a MATCH state to the END state, or because the alignment passed through DELETE states.

hmmprofalign(..., 'PropertyName', PropertyValue,...) defines optional properties using property name/value pairs.

hmmprofalign(..., 'ShowScore', ShowScoreValue), when ShowScoreValue is true, displays the scoring space and the winning path.

hmmprofalign(..., 'Flanks', FlanksValue), when FlanksValue is true, includes the symbols generated by the FLANKING INSERT states in the output sequence.

hmmprofalign(..., 'ScoreFlanks', ScoreFlanksValue), when ScoreFlanksValue is true, includes the transition probabilities for the flanking states in the raw score.

hmmprofalign(..., 'ScoreNullTransitions', ScoreNullTransitionValue), when ScoreNullTransitionsValue is true, adjusts the raw score using the null model for transitions (Model.NullX).

Note   Multiple target alignment is not supported in this implementation. All the Model.LoopX probabilities are ignored.

Examples

load('hmm_model_examples','model_7tm_2') % load a model example
load('hmm_model_examples','sequences')  % load a sequence example
SCCR_RABIT=sequences(2).Sequence; 
[a,s]=hmmprofalign(model_7tm_2,SCCR_RABIT,'showscore',true)

See Also

Bioinformatics Toolbox™ functions gethmmprof, hmmprofestimate, hmmprofgenerate, hmmprofgenerate, hmmprofstruct, pfamhmmread, showhmmprof, multialign, profalign

graphtraverse

hmmprofestimate