| Bioinformatics Toolbox | |
Display characteristics for amino acid sequences
proteinplot(SeqAA)
SeqAA | Amino acid sequence or a structure with a field Sequence containing an amino acid sequence. |
proteinplot is a tool for analyzing a single amino acid sequence. You can use the results from proteinplot to compare the properties of several amino acid sequences. It displays smoothed line plots of various properties such as the hydrophobicity of the amino acids in the sequence.
Importing sequences into proteinplot
In the MATLAB Command Window, type
proteinplot(Seq_AA)
The proteinplot interface opens and the sequence Seq_AA is shown in the Sequence text box.
Alternatively, type or paste an amino acid sequence into the Sequence text box.
You can can import a sequence with the Import dialog box.
Click the Import Sequence button. The Import dialog box opens.
From the Import From list, select, a variable in the MATLAB workspace, ASCII text file, FASTA formatted file, GenPept formatted file, or accession number in the GenPept database.
Information about the properties
You can also access information about the properties from the Help menu.
From the Help menu, click References. The Help Browser opens with a list of properties and references.
Scroll down to locate the property you are interested in studying.
Working with Properties
When you click on a property a smoothed plot of the property values along the sequence will be displayed. Multiple properties can be selected from the list by holding down Shift or Ctrl while selecting properties. When two properties are selected, the plots are displayed using a PLOTYY-style layout, with one Y axis on the left and one on the right. For all other selections, a single Y axis is displayed. When displaying one or two properties, the Y values displayed are the actual property values. When three or more properties are displayed, the values are normalized to the range 0-1.
You can add your own property values by clicking on the Add button next to the property list. This will open up a dialog that allows you to specify the values for each of the amino acids. The Display Text box allows you to specify the text that will be displayed in the selection box on the main proteinplot window. You can also save the property values to an m-file for future use by typing a file name into the Filename box.
The Terminal Selection boxes allow you to choose to plot only part of the sequence. By default all of the sequence is plotted. The default smoothing method is an unweighted linear moving average with a window length of five residues. You can change this using the "Configuration Values" dialog from the Edit menu. The dialog allows you to select the window length from 5 to 29 residues. You can modify the shape of the smoothing window by changing the edge weighting factor. And you can choose the smoothing function to be a linear moving average, an exponential moving average or a linear Lowess smoothing.
The File menu allows you to Import a sequence, save the plot that you have created to a FIG file, you can export the data values in the figure to a workspace variable or to a MAT file, you can export the figure to a normal figure window for customizing, and you can print the figure.
The Edit menu allows you to create a new property, to reset the property values to the default values, and to modify the smoothing parameters with the Configuration Values menu item.
The View menu allows you to turn the toolbar on and off, and to add a legend to the plot.
The Tools menu allows you to zoom in and zoom out of the plot, to view Data Statistics such as mean, minimum and maximum values of the plot, and to normalize the values of the plot from 0 to 1.
The Help menu allows you to view this document and to see the references for the sequence properties built into proteinplot
Bioinformatics Toolbox functions aacount, atomiccomp, msalign
MATLAB function plotyy
| | probesetvalues | prune (phytree) | |
© 1994-2005 The MathWorks, Inc.