EMBOSS: cpgplot

| ## 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