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Displays a set of HMM profile alignments


hmmprofmerge(Sequences, Names)
hmmprofmerge(Sequences, Names, Scores)


SequencesArray of sequences. Sequences can also be a structured array with the aligned sequences in a field Aligned or Sequences, and the optional names in a field Header or Name.

Names for the sequences. Enter a cell array of character vectors.


Pairwise alignment scores from the function hmmprofalign. Enter a vector of values with the same length as the number of sequences in Sequences.


hmmprofmerge(Sequences) opens your default Web browser and displays a set of prealigned sequences to an HMM model profile. The output is aligned corresponding to the HMM states.

  • Match states — Uppercase letters

  • Insert states — Lowercase letters or asterisks (*)

  • Delete states — Dashes

Periods (.) are added at positions corresponding to inserts in other sequences. The input sequences must have the same number of profile states, that is, the joint count of capital letters and dashes must be the same.

hmmprofmerge(Sequences, Names) labels the sequences with Names.

hmmprofmerge(Sequences, Names, Scores) sorts the displayed sequences using Scores.


load('hmm_model_examples','model_7tm_2')  %load model
load('hmm_model_examples','sequences')  %load sequences

for ind =1:length(sequences)
    [scores(ind),sequences(ind).Aligned] =...
hmmprofmerge(sequences, scores)

Introduced before R2006a

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