hmmprofmerge

Concatenate prealigned strings of several sequences to profile hidden Markov model (HMM)

Syntax

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

Arguments

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

Names for the sequences. Enter a vector of names.

Scores

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

Description

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.

Examples

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] =...
        hmmprofalign(model_7tm_2,sequences(ind).Sequence);
    end
hmmprofmerge(sequences, scores)
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