dotpath

dotpath

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dotpath displays a non-overlapping wordmatch dotplot of two sequences. dotpath is very similar to the program dottup, which looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of those words.

Here is a sample session with dotpath:

% dotpath embl:AF129756 embl:AP000504 -word 20 Displays a non-overlapping wordmatch dotplot of two sequences Graph type [x11]:

Mandatory qualifiers (bold if not always prompted):

[-sequencea] (sequence)

Sequence USA.

[-sequenceb] (sequence)

Sequence USA.

-wordsize (integer)

Word size.

-graph (graph)

Graph type.

-outfile (outfile)

Output filename.

Optional qualifiers:

-overlaps (boolean)

Displays the overlapping matches (in red) and the minimal set of non-overlapping matches.

-[no]boxit (boolean)

Draw a box around dotplot.

Advanced qualifiers:

-data (boolean)

Output the match data to a file instead of plotting it.