A window of specified length is moved up all possible diagonals and a score is calculated within each window for each position along the diagonals. The score is the sum of the comparisons of the two sequences using the given similarity matrix along the window. If the score is above the threshold, then a line is plotted on the image over the position of the window. Here is a sample session with dotmatcher. An image is output to the requested graphics device.
Data files It uses the specified matrix substitution file to compare the two sequences.
Others can be specified. Users can provide their own data files in their own directories. Diagnostic Error Messages None. Exit status 0 upon successful completion. Known bugs None.