wobble

wobble

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wobble plots the third position variability as an indicator of a potential coding region.

Here is a sample session with wobble. The example sequence is from Pseudomonas aeruginosa, which has a high G+C content and a very biased third codon position. If it can be G or C, it usually is:

% wobble Wobble base plot Input sequence: embl:paamir Graph type [x11]: Output file [paamir.wobble]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

-graph (xygraph)

Graph type.

-outf (outfile)

Output filename.

Optional qualifiers:

-window (integer)

Window size in codons.

Advanced qualifiers:

-bases (string)

Bases used.