Install dotter by entering the following commands in the terminal:
sudo apt update sudo apt install dotter
detailed comparison of two genomic sequences
Dotter is a graphical dot-matrix program for detailed comparison of two sequences. . * Every residue in one sequence is compared to every residue in the other, and a matrix of scores is calculated. * One sequence is plotted on the x-axis and the other on the y-axis. * Noise is filtered out so that alignments appear as diagonal lines. * Pairwise scores are averaged over a sliding window to make the score matrix more intelligible. * The averaged score matrix forms a three-dimensional landscape, with the two sequences in two dimensions and the height of the peaks in the third. This landscape is projected onto two dimensions using a grey-scale image - the darker grey of a peak, the higher the score is. * The contrast and threshold of the grey-scale image can be adjusted interactively, without having to recalculate the score matrix. * An Alignment Tool is provided to examine the sequence alignment that the grey-scale image represents. * Known high-scoring pairs can be loaded from a GFF file and overlaid onto the plot. * Gene models can be loaded from GFF and displayed alongside the relevant axis. * Compare a sequence against itself to find internal repeats. * Find overlaps between multiple sequences by making a dot-plot of all sequences versus themselves. * Run Dotter in batch mode to create large, time-consuming dot-plots as a background process.