TOADS

TOpologies in Alignments of DNA Sequences

Download the file example2.dat.gz and unzip it. You will get an alignment of 4 DNA sequences, 25077 nucleotides long. Apply TOADS as described before. You can, in principle, plot the results with MATLAB program plot_toads.m as in the previous example. However, since the alignment is rather long and has 3556 topology-defining sites, this is not particularly useful for discerning patterns in the sequence alignment. It is better to use MATLAB program window_toads.m. This program moves a window of specified length WIN with a specified step size STEP along the alignment. For each window position the program computes and plots the

• average proportion of topology-defining sites,
• average proportion of sites supporting topology 1,
• average proportion of sites supporting topology 2,
• average proportion of sites supporting topology 3.

The plots suggest that there are two recombinant regions, 3100-9500 and 11000-22000, where a transition from topology 1 into topology 3 has occurred. These recombination events are accompanied by a noticeable reduction in the nucleotide substitution rate, as indicated by the drop in the proportion of topology-defining sites in the regions affected by recombination.

Back to the main page
Last modified: August 2003