The Protein Analysis Toolbox command allows you to analyze the properties of a protein sequence. As well as such algorithms as hydrophobicity, secondary structure and antigenicity plots, the first profile Amino Acid Properties allows you to calculate various statistics about the whole sequence. Such as amino acid composition, pI, molecular weight extinction coefficient and aliphatic index.
1. Choose Analyze | Protein Analysis Toolbox.
2. Scroll through the Protocol list and select the profile you want to calculate.
When a profile is selected, a brief description of it is displayed in the text panel to the right of the Protocol list.
3. Select the List and Plot check boxes as necessary, for a text listing or graphical view of the results.
To select or deselect all checkboxes in a column, hold down the option key while clicking on any checkbox in the column.
4. Repeat steps 2 and 3 for each profile you want to calculate.
5. Choose the portion of the sequence that you want to analyse by typing in the sequence numbers that bracket the region in the Region text boxes. Alternatively, select a region from the features table drop-down menu to the right of the text boxes.
Some profiles require a minimum sequence length, or window, for their calculation. A selection smaller than this value is the most common cause of the calculation failing.
6. If you want to restore the MacVector default settings, select Defaults.
7. Select OK to perform the analysis.
The OK button will only be enabled if at least one View or Plot checkbox is selected.
The results of the analysis are displayed automatically.
Plots generated by selecting the Plot check box are displayed in a graphical window. Numerical results generated by selecting the List check box are displayed as tables in a scrollable text window.