Base composition

When a DNA sequence is the active window, one or more property profiles can be calculated for the sequence.

1. Choose Analyze | Base Composition.
2. Select one or more check boxes in the List panel to generate a text listing of the required mono-, di- and trinucleotide frequencies and temperature information.
3. Select the Base composition check box to generate percentage composition plots.
4. Specify the required composition plots by selecting Options in the Plot panel.
5. Select the temperature profile check box to generate a running average of the sequence Tm or Td.
6. Specify temperature profile parameters in the Temperature parameters panel as follows:
7. choose Tm or Td from the Calculate drop-down menu
8. choose the duplex type from the adjacent drop-down menu
9. - enter a value in the nucleic acid conc. text box
10. - enter a value in the cation conc. text box.
11. Type a value in the window size text box for the number of residues over which properties are calculated.
12. Select the required check boxes in the Histograms panel to generate histograms for di- and trinucleotide repeats along the sequence.
13. Specify the required Nucleotide frequency histograms by selecting Options to the right of each check box.
14. If required, you can restrict the analysis to a portion of the sequence, 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.
15. Select OK

Nucleotide frequency histograms

The frequency of occurence of di- and trinucleotides is visualized in MacVector using a histogram plot, where each histogram bar represents the number of occurences of the selected set of nucleotides, within a region of the sequence whose length is determined by the number of bars you choose to plot on the histogram.

Base composition plots

When base composition plots are generated, MacVector can generate up to six separate graphs, each with a maximum of four plots.

1. Choose Analyze | Base Composition.

The Base Composition Analysis dialog box is displayed.

2. Select Options in the Plot panel.

The Base Composition Plotting Options dialog box is displayed.

3. Enter the required composition plot for the first graph, either by typing one or more base characters in the Panel 1 / Plot 1 text box, or by choosing from the options on the drop-down menu to the right of the text box.

When a valid entry is made, the following changes occur:

- a second text box appears, under the Plot 2 position

- a new text box appears in the Panel 2 row, at the Plot 1 position.

The Panel rows refer to separate graphs, the Plot columns to plots on each graph.

4. Enter additional composition plots as required.

Each time an extra plot is specified for a given panel, a new text box appears under the next plot column, up to the maximum 4 plots. When the first plot for a panel is specified, a new row appears, up to the maximum 6 panels.

5.To change the color of each plot, do one of the following:

- Click on the arrow button to the right of the color swatch, and choose from the displayed color palette

- Click on the color swatch itself, and use the system Color Picker; this is useful for fine control.

6. Select OK to remove the Base Composition Plotting Options dialog box.

7. Select OK to generate the plots.

TO SPECIFY nucleotide frequency histograms

1. Choose Analyze | Base Composition.

The Base Composition Analysis dialog box is displayed.

2. Select Options in the Histograms panel next to the dinucleotide or trinucleotide check box.

Depending on which Options was selected, either the Dinucleotide or Trinucleotide Histogram Options dialog box is displayed.

3. Enter either the 2 or 3 letters that represent the di- or trinucleotide sequence in the Panel text boxes.

Up to 6 histograms can be generated for dinucleotides and trinucleotides. As each histogram is specified, a new panel row appears, up to the maximum allowed.

4. Enter the number of bars required for each histogram in the Plot text box.

The sequence being analyzed is split into equal parts, and the number of occurrences of the nucleotide sequence in each part is represented by a bar on the histogram.

5. If you need to change the bar color, do one of the following:

- Click on the arrow button to the right of the color swatch, and choose from the displayed color palette

- Click on the color swatch itself, and use the system Color Picker; this is useful for fine control.

6. Select OK to remove the Histogram Options dialog box.

7. Select OK to generate the histograms.

Related Topics.

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