multialignwrite
Write multiple alignment to file
Syntax
multialignwrite(
File
, Alignment
)
multialignwrite(..., 'Format', FormatValue
,
...)
multialignwrite(..., 'Header', HeaderValue
,
...)
multialignwrite(..., 'WriteCount', WriteCountValue
,
...)
Description
multialignwrite(
writes
the contents of an alignment to a ClustalW ALN-formatted (default)
or MSF-formatted file.File
, Alignment
)
multialignwrite(..., '
calls PropertyName
', PropertyValue
,
...)multialignwrite
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:
multialignwrite(..., 'Format',
specifies the format of the file. FormatValue
,
...)FormatValue
can
be 'ALN'
(default) or 'MSF'
.
multialignwrite(..., 'Header',
specifies the first line of the file. The default
for HeaderValue
,
...)HeaderValue
is 'MATLAB multiple
sequence alignment'
.
multialignwrite(..., 'WriteCount',
specifies whether to add the residue counts to the
end of each line. WriteCountValue
,
...)WriteCountValue
can be true
(default)
or false
.
Input Arguments
|
An alignment, such as returned by the |
|
Character vector or string specifying either a file name or a path and file name for saving the data. If you specify only a file name, the file is saved to the MATLAB® Current Folder browser. Tip If you use an Below the columns of the ClustalW ALN-formatted file, symbols can appear that denote:
For more information on these symbols and the groups of residues considered conserved and
semiconserved, see section 12 in “Changes since version 1.6”
at |
|
Character vector or string that specifies the format of Tip You can also write to an MSF-formatted file by using an |
|
Character vector or string that specifies the first line of the file. Tip Use the Default: |
|
Specifies whether to add the residue counts to the end of each
line. Choices are |
Examples
Use the
fastaread
function to readp53samples.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)
Version History
Introduced in R2008b
See Also
fastaread
| fastawrite
| gethmmalignment
| multialign
| multialignread
| seqalignviewer
| phytreewrite
| seqconsensus
| seqdisp
| seqprofile