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

Syntax

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

Arguments

`Sequences`	Array 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) 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)

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

Syntax

Arguments

Description

Examples

See Also

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