dotter is a graphical tool for visualising the relationship between two sequences,which can be either DNA or protein. Dotter is a 'tool of best choice' for some problems, including locating and assesing repeats, and aligning proteins visually o�nto DNA. The sensitivity can be dynamically regulated, and is based o�n Karlin-Altschul statistics. Dotter requires an X11 display.

dotter is very useful for finding:

• overlaps between sequences.
• overlap between contigs in a sequencing project.
• visually identifying repeat sequences within a sequence.
• overlaps with known sequences (eg. vectors, transposons, other genes etc).

Why is dotter a good dotplot program?

• A threshold above which a dot is plotted can be set interactively. This allows the user to vary the signal/noise ratio easily. In many other dotplot programs, you have to re-run the program each time you re-define the threshold value.
• Dotter shows a sliding alignment of your sequences. If you move the cursor within the dotplot output, the sequences in the alignment box re-align accordingly (easier to see than to explain!).
• Dotter can be run, and the output saved to be viewed later.
• You can compare a number of sequences with each other simultaneously using dotter. This is particularly useful if you are looking at a series of sequences and looking for overlap between them, or repeats within them.

The command line usage for dotter is in the following format:
dotter [options] query_seq subject_seq [X options]

Format of the query and subject sequences must be in Fasta or raw format.

Options on the command can be:

• -b Batch mode, write dotplot to -l Load dotplot from -m Memory usage limit in Mb (default 0.5)
• -z Set zoom (compression) factor
• -p Set pixel factor manually (ratio pixelvalue/score)
• -W Set sliding window size. (K => Karlin/Altschul estimate)
• -M Read in score matrix from (Blast format; Default: Blosum62)
• -f Read feature segments from -i Do NOT use installed private colormap, but share with other apps
• -r Reverse and complement horizontal_sequence (DNA vs Protein)
• -D Don't display mirror image in self comparisons
• -w For DNA: horizontal_sequence top strand o�nly (Watson)
• -c For DNA: horizontal_sequence bottom strand o�nly (Crick)
• -q Horizontal_sequence offset
• -s Vertical_sequence offset

The most important X options are:

• -acefont < font> Main font.
• -font < font> Menu font.

(Any standard X option can also be used, such as -bg green -fg red.)

Example command line usage:

run dotter to compare sequence1.tfa and sequence2.tfa
dotter sequence1.tfa sequence2.tfa

run dotter and save the results to results.file
dotter -bresults.file sequence1.tfa sequence2.tfa

View results.file
dotter -lresults.file sequence1.tfa sequence2.tfa

More information o�n using dotter: Dotter's Home and UVic, Canada

Related resources from the Sonhammer group see: http://sonnhammer.sbc.su.se/databases.html

References:
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis Erik L.L. Sonnhammer and Richard Durbin Gene 167:GC1-10 (1995) [Entrez]