syco

syco

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syco is a frame-specific gene finder that tries to recognize protein coding sequences by virtue of the similarity of their codon usage to a codon frequency table.

Here is a sample session with syco, requesting graphical output:

% syco -plot -cfile pae Synonymous codon usage Gribskov statistic plot Input sequence: embl:paamir Graph type [x11]:

It is essential to use the correct codon usage file for the species.

Mandatory qualifiers (bold if not always prompted):

[-sequence] (sequence)

Sequence USA.

-graph (xygraph)

Graph type.

-outfile (outfile)

Output filename.

Advanced qualifiers:

-cfile (codon)

Codon usage file.

-window (integer)

Averaging window.

-uncommon (boolean)

Show common codon usage.

-minimum (float)

Minimum value for a common codon.

-plot (boolean)

Produce plot.