
                              EMBOSS: cpgplot
     _________________________________________________________________
   
                                Program cpgplot
                                       
Function

   Plot CpG rich areas
   
Description

   CpG refers to a C nucleotide immediately followed by a G. The 'p' in
   'CpG' refers to the phosphate group linking the two bases.
   
   Detection of regions of genomic sequences that are rich in the CpG
   pattern is important because such regions are resistant to methylation
   and tend to be associated with genes which are frequently switched on.
   Regions rich in the CpG pattern are known as CpG islands.
   
   It has been estimated that about half of all mammalian genes have a
   CpG-rich region around their 5' end. It is said that all mammalian
   house-keeping genes have a CpG island!
   
   Non-mammalian vertebrates have some CpG islands that are associated
   with genes, but the association gets equivocal in the farther
   taxonomic groups.
   
   Finding a CpG island upstream of predicted exons or genes is good
   contributory evidence.
   
   By default, this program defines a CpG island as a region where, over
   an average of 10 windows, the calculated % composition is over 50% and
   the calculated Obs/Exp ratio is over 0.6 and the conditions hold for a
   minimum of 200 bases. These conditions can be modified by setting the
   values of the appropriate parameters.
   
   The Expected number of CpG patterns in a window is calculated as the
   number of 'C's in the window multiplied by the number of 'G's in the
   window, divided by the window length.
   
   This program reads in one or more sequences and calculates the Obs/Exp
   ratio, the percentage CpG over a window which is moved along the
   sequence. These calculated values can be plotted, together with the
   regions which match this program's definition of a CpG island.
   
Usage

   Here is a sample session with cpgplot.

% cpgplot embl:rnu68037
Plot CpG rich areas
Window size [100]:
Shift increment [1]:
Minimum Length [200]:
Minimum observed/expected [0.6]:
Minimum percentage [50.]:
Output file [rnu68037.cpgplot]:
Graph type [x11]:

   click here for result
   
Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -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
                                  postition that the window is moved to.
   -shift              integer    This determines the number of bases that the
                                  window is moved each time after values of
                                  the percentage CG content and the Observed
                                  frequency of CG are calculated within the
                                  window.
   -minlen             integer    This sets the minimum length that a CpG
                                  island has to be before it is reported.
   -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.
   -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.
  [-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.
  [-graph]             xygraph    Graph type

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]obsexp         bool       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.
   -[no]cg             bool       If this is set to true then the graph of the
                                  regions which have been determined to be
                                  CpG islands is displayed.
   -[no]pc             bool       If this is set to true then the graph of the
                                  percentage C plus G within a window is
                                  displayed.
   -featout            featout    File for output features

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -window 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 postition that the window is moved to. Integer 1 or more 100
   -shift This determines the number of bases that the window is moved
   each time after values of the percentage CG content and the Observed
   frequency of CG are calculated within the window. Integer 1 or more 1
   -minlen This sets the minimum length that a CpG island has to be
   before it is reported. Integer 1 or more 200
   -minoe 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. Number from 0.000 to 10.000 0.6
   -minpc This sets the minimum average percentage of G plus C a set of
   10 windows that are required before a CpG island is reported. Number
   from 0.000 to 100.000 50.
   [-outfile]
   (Parameter 2) 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. Output file <sequence>.cpgplot
   [-graph]
   (Parameter 3) Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -[no]obsexp 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. Yes/No
   Yes
   -[no]cg If this is set to true then the graph of the regions which
   have been determined to be CpG islands is displayed. Yes/No Yes
   -[no]pc If this is set to true then the graph of the percentage C plus
   G within a window is displayed. Yes/No Yes
   -featout File for output features Writeable feature table unknown.gff
   
Input file format

   Any DNA sequence USA.
   
Output file format

   The output file from the above example (rnu68037.cpgplot) follows:

CPGPLOT islands of unusual CG composition
RNU68037 from 51 to 1168

     Observed/Expected ratio > 0.60
     Percent C + Percent G > 50.00
     Length > 200

 Length 233 (157..389)

 Length 310 (654..963)

   The first non-blank line of the output file is the title of the output
   file. It is followed by the name of the sequence and the region
   analysed (from the centre of the first window to the centre of the
   last window). The conditions for specifying a CpG island follow
   (Observed/Expected ratio, Percent C + Percent G, Length).
   
   The length and start and end positions of any predicted CpG islands
   are then output.
   
Data files

   None.
   
Notes

   None.
   
References

   The original program was described in:
   
   Larsen F, Gundersen G, Lopez R, Prydz H "CpG islands as gene markers
   in the human genome." Genomics 1992 Aug;13(4):1095-107
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 if successful.
   
Known bugs

   None.
   
See also

   Program name                          Description
   cpgreport    Reports all CpG rich regions
   geecee       Calculates the fractional GC content of nucleic acid sequences
   newcpgreport Report CpG rich areas
   newcpgseek   Reports CpG rich regions
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

Completed 23rd March 1999.
Last modified 28th July 1999.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
