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

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or
       directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package.
       It can be redistributed under the same terms as EMBOSS itself.