multialignviewer - Display and interactively adjust multiple sequence alignment

Syntax

multialignviewer multialignviewer(Alignment) multialignviewer('close') multialignviewer(..., 'Alphabet', AlphabetValue, ...) multialignviewer(..., 'SeqHeaders', SeqHeadersValue, ...)

Description

multialignviewer opens the Multiple Sequence Alignment Viewer window, where you can display and interactively adjust a multiple sequence alignment.

multialignviewer(Alignment) loads a group of previously multiply aligned sequences into the Multiple Sequence Alignment Viewer window, where you can view and interactively adjust the alignment.

multialignviewer('close') closes the Multiple Sequence Alignment Viewer window.

multialignviewer(..., 'PropertyName', PropertyValue, ...) calls multialignviewer with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Enclose each PropertyName in single quotation marks. Each PropertyName is case insensitive. These property name/property value pairs are as follows:

multialignviewer(..., 'Alphabet', AlphabetValue, ...) specifies the alphabet type for the sequences.

multialignviewer(..., 'SeqHeaders', SeqHeadersValue, ...) specifies a list of names to label the sequences in the Multiple Sequence Alignment Viewer window.

Inputs

Alignment

Group of multiply aligned amino acid or nucleotide sequences specified by one of the following:

MATLAB structure containing a Sequence field, such as returned by fastaread, gethmmalignment, multialign, or multialignread
MATLAB character array that contains a multiple sequence alignment, such as returned by multialign
String specifying a file name, path and file name, or URL pointing to a file, where the file contains a multiple sequence alignment
3-by-N character array showing the pairwise alignment of two sequences, such as returned by nwalign or swalign

AlphabetValue

String that specifies the alphabet type for the sequences. Choices are 'AA' for amino acids or 'NT' for nucleotides. If you do not specify an alphabet type, multialignviewer attempts to determine the correct alphabet. If it cannot, it defaults to 'AA'.

SeqHeadersValue

List of names to label the sequences in the Multiple Sequence Alignment Viewer window, specified by either of the following:

MATLAB array of structures containing a Header or Name field, such as returned by fastaread, gethmmalignment, multialign, or multialignread
Cell array of strings

SeqHeadersValue must contain the same number of elements as there are sequences in Alignment.

Examples

Load a file containing a multiple sequence alignment in the Multiple Sequence Alignment Viewer window, then close the window:

% Load multiple sequence alignment file
% in Multiple Sequence Alignment Viewer
multialignviewer('aagag.aln')

% Close Multiple Sequence Alignment Viewer window
multialignviewer('close')

Alternatives

You can also display a color-coded multiple or pairwise sequence alignment using the showalignment function. However, the alignment displays in a MATLAB Figure window, where you cannot interact with it.