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Plot base composition

When a sequence is read into the program its composition is displayed in the text output window to provide a simple check that the data has been read correctly. The values can also be requested from the "Statistics" menu and the results are displayed as shown below.

Wed 12 Nov 17:10:25 1997: base composition
A 1966 (24.17%) C 1996 (24.54%) G 2185 (26.86%) T 1987 (24.43%) - 0 (0.00%)

The composition of the sequence can be displayed graphically. A window is slid along the sequence one base at a time, and at each point the number of occurrences of each selected base type is counted and plotted. Users can select which base types are counted, the size of the window used and the region of the sequence to analyse.

(Click for full size image)

For example the A and T composition can be plotted by selecting base types A and T in the dialogue. As usual the values can also be listed in the text output window. Note that this "result", i.e. the base composition counts for every position along the sequence, will persist until the user explicitly removes it. To save memory delete results as soon as they are no longer required.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.