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

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EMBOSS 6.4.0                                       05/11/2012                                        CPGPLOT(1e)

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).

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

Inputsection-sequenceseqallRequiredsection-windowinteger
           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

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

       -minoefloat
           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

       -minpcfloat
           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.

   Outputsection-outfileoutfile
           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.

       -plottoggle
           Default value: Y

       -graphxygraph-obsexpboolean
           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

       -cgboolean
           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

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

       -outfeatfeatout
           File for output features

       cpgplot is fully documented via the tfm(1) system.

cpgplot-sequenceseqall-windowinteger-minleninteger-minoefloat-minpcfloat-outfileoutfile-plottoggle-graphxygraph-obsexpboolean-cgboolean-pcboolean-outfeatfeatoutcpgplot-help