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.

dottup 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 these words.

Here is a sample session with dottup :

% dottup embl:eclac embl:eclaci -wordsize=6 -gtitle="eclaci vs eclac"

Mandatory qualifiers ( bold if not always prompted):

[-sequencea] (sequence)

Sequence USA.

[-sequenceb] (sequence)

Sequence USA.

-wordsize (integer)

Word size.

- data (boolean)

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

- graph (graph)

Graph type.

- xygraph (xygraph)

Graph type.

- outfile (outfile)

Output filename.

Optional qualifiers ( bold if not always prompted):

- [no]boxit (boolean)

Draw a box around dotplot.

Advanced qualifiers:

-stretch (boolean)

Use nonproportional axes.

dreg searches for matches of a regular expression to a nucleic acid sequence.

Here is a sample session with dreg :

% dreg
Input sequence: embl:paamir
Output file [paamir.dreg]: 
Regular expression pattern: ggtacc

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-pattern] (regexp)

Regular expression pattern.

[-outfile] (outfile)

Output filename.