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PROGRAM:

NAME

cpgplot - Identify and plot CpG islands in nucleotide sequence(s)

SYNOPSIS

cpgplot -sequence seqall -window integer -minlen integer -minoe float -minpc float
-outfile outfile -plot toggle -graph xygraph -obsexp boolean -cg boolean
-pc boolean -outfeat featout

cpgplot -help

DESCRIPTION

cpgplot is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Nucleic:CpG Islands" command group(s).

OPTIONS

Input section
-sequence seqall

Required section
-window integer
The percentage CG content and the Observed frequency of CG is calculated within a
window whose size is set by this parameter. The window is moved down the sequence and
these statistics are calculated at each position that the window is moved to. Default
value: 100

-minlen integer
This sets the minimum length that a CpG island has to be before it is reported.
Default value: 200

-minoe float
This sets the minimum average observed to expected ratio of C plus G to CpG in a set
of 10 windows that are required before a CpG island is reported. Default value: 0.6

-minpc float
This sets the minimum average percentage of G plus C a set of 10 windows that are
required before a CpG island is reported. Default value: 50.

Output section
-outfile outfile
This sets the name of the file holding the report of the input sequence name, CpG
island parameters and the output details of any CpG islands that are found.

-plot toggle
Default value: Y

-graph xygraph

-obsexp boolean
If this is set to true then the graph of the observed to expected ratio of C plus G to
CpG within a window is displayed. Default value: Y

-cg boolean
If this is set to true then the graph of the regions which have been determined to be
CpG islands is displayed. Default value: Y

-pc boolean
If this is set to true then the graph of the percentage C plus G within a window is
displayed. Default value: Y

-outfeat featout
File for output features

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