Bioinformatics Toolbox™

multialignwrite - Write multiple alignment to file using ClustalW ALN format

Syntax

multialignwrite(File, Alignment) multialignwrite(..., 'Header', HeaderValue, ...) multialignwrite(..., 'WriteCount', WriteCountValue, ...)

Arguments

File String specifying either a file name or a path and file name for saving the ClustalW ALN-formatted data. If you specify only a file name, the file is saved to the MATLAB Current Directory.

Alignment

An alignment, such as returned by the multialign function, represented by either a:

Vector of structures, each containing the fields Header and Sequence.
Character array

HeaderValue

String that specifies the first line of the file. Default is 'MATLAB multiple sequence alignment'.

Tip Use the 'Header' property if your file header needs to be a specific format for a third-party software application.

WriteCountValue Determines whether to add the residue counts to the end of each line. Choices are true (default) or false.

Description

multialignwrite(File, Alignment) writes the contents of Alignment to File, a ClustalW ALN-formatted file.

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

multialignwrite(..., 'Header', HeaderValue, ...) specifies the first line of the file. Default is 'MATLAB multiple sequence alignment'.

Tip Use the 'Header' property if your file header needs to be a specific format for a third-party software application.

multialignwrite(..., 'WriteCount', WriteCountValue, ...) determines whether to add the residue counts to the end of each line. Choices are true (default) or false.

Note Below the columns of the ClustalW ALN-formatted file, symbols may appear that denote:

* — Residues or nucleotides in the column are identical in all sequences in the alignment.
: — Conserved substitutions exist in the column for all sequences in the alignment.
. — Semiconserved substitutions exist in the column for all sequences in the alignment.

For more information on these symbols, see http://www.ebi.ac.uk/help/formats.html#aln.

For more information on the groups of residues considered conserved and semiconserved, see section 12 of "Changes since version 1.6" at http://web.mit.edu/clustalw_v1.83/README.

Examples

Use the fastaread function to read p53samples.txt, a FASTA-formatted file included with the Bioinformatics Toolbox software, which contains seven cellular tumor antigen p53 sequences.
```
p53 = fastaread('p53samples.txt')

p53 = 

7x1 struct array with fields:
    Header
    Sequence
```
Use the multialign function to align the seven cellular tumor antigen p53 sequences.
```
ma = multialign(p53,'verbose',true);
```
Write the alignment to a file named p53.aln.
```
multialignwrite('p53.aln',ma)
```

multialignwrite - Write multiple alignment to file using ClustalW ALN format

Syntax

Arguments

Description

Examples

See Also