| Bioinformatics Toolbox | |
Display a sequence alignment with color
showalignment(Alignment, 'PropertyName', PropertyValue) showalignment(..., 'StartPointers', StartPointersValue) showalignment(..., 'MatchColor', MatchColorValue) showalignment(..., 'SimilarColor' SimilarColorValue) showalignment(..., 'Columns', ColumnsValue)
Alignment | Enter the output from either the function swalign or nwalign. |
| SimilarColorValue | Property to specify the starting indices of the aligned sequences. StartPointers is the two element vector returned as the third output of the function swalign. |
| MatchColorValue | Property to select the color to highlight matching characters. Enter a 1-by-N RGB vector specifying the intensity (0 to 255) of the red, green, and blue components, or enter a character from the following list: 'b'– blue, 'g'– green, 'r'– red, 'c'– cyan, 'm'– magenta, or 'y'– yellow. The default color is red, 'r'. |
SimilarColorValue | Property to select the color to highlight similar characters. Enter a 1-by-3 RGB vector or color character. The default color is magenta. |
ColumnsValue | Property to specify the number of characters in a line. Enter the number of characters to display in one row. The default value is 64. |
showalignment(Alignment, 'PropertyName', PropertyValue) displays an alignment string with matches and similar residues highlighted with color.
showalignment(..., 'StartPointers', StartPointersValue) specifies the starting indices in the original sequences of a local alignment.
showalignment(..., 'MatchColor', MatchColorValue) selects the color to highlight the matches in the output display. The default color is red. For example, to use cyan, enter 'c' or [0 255 255].
showalignment(..., 'SimilarColor' SimilarColorValue) selects the color to highlight similar residues that are not exact matches. The default color is magenta.
showalignment(..., 'Columns', ColumnsValue) specifies how many columns per line to use in the output, and labels the start of each row with the sequence positions.
Enter two amino acid sequences and show their alignment.
[Score, Alignment] = nwalign('VSPAGMASGYD','IPGKASYD');
showalignment(Alignment);
Bioinformatics Toolbox functions nwalign, swalign
| | seqwordcount | showhmmprof | |
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