EMBOSS: cpgreport

| ## EMBOSS: cpgreport

# Program cpgreport

## Function

Reports all CpG rich regions

## Description

cpgreport scans a nucleotide sequence for regions with higher than expected frequencies of the dinucleotide CG.

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.

This program does not find CpG islands as normally defined: "a region of greater than 200 bp with a %GC of greater than 50% and observed/expected CpG > 0.6". cpgreport instead uses a running sum rather than a window to create the score as follows: if not CpG at position i, then decrement running-Sum counter, but if CpG then running-Sum counter is incremented by the CPGSCORE. Spans greater than the threshold are searched for recursively.

## Usage

Here is a sample session with cpgreport.

    % cpgreport embl:rnu68037
    Reports CpG rich regions
    CpG score [17]:
    Output file [rnu68037.cpgreport]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -score              integer    This sets the score for each CG sequence
                                      found. A value of 17 is more sensitive, but
                                      28 has also been used with some success.
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -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
-score | This sets the score for each CG sequence found. A value of 17 is more sensitive, but 28 has also been used with some success. | Integer from 1 to 200 | 17
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.cpgreport
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-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.cpgreport) follows:

    CPGREPORT of RNU68037 from 1 to 1218

    Sequence              Begin    End Score        CpG   %CG  CG/GC
    RNU68037                 12     13    17          1 100.0    -
    RNU68037                 47     48    17          1 100.0    -
    RNU68037                 96   1032   630         87  66.1   0.65
    RNU68037               1072   1100    26          3  62.1   0.00
    RNU68037               1139   1140    17          1 100.0    -
    RNU68037               1183   1193    26          2  72.7   2.00

The first non-blank line of the output file is the title line giving the program name, the name of sequence being analysed and the start and end positions of the sequence.

The second non-blank line contains the headings of teh columns.

Subsequent lines contain columns with the following information:

- The name of the sequence.
- The begin position and the end position of the CpG-rich region.
- The score of the CpG-rich region.
- The number of CpG's in the CpG-rich region.
- The %(G+C) in the CpG-rich region.
- The ratio of CpG to GpC in the CpG-rich region.

If the count of GpC in the region is zero, then the ratio of CG/GC is reported as '-'.

## Data files

None.

## Notes

This program does not find CpG islands as normally defined (see cpgplot).

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 if successful.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cpgplot | Plot CpG rich areas
geecee | Calculates the fractional GC content of nucleic acid sequences
newcpgreport | Report CpG rich areas
newcpgseek | Reports CpG rich regions

## Author(s)

This program was originally written by Gos Micklem (E-mail: gos@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK).

It was modified for inclusion in EGCG under the name 'CPGSPANS' by Rodrigo Lopez S. (E-mail: rls@ebi.ac.uk Post: EMBL Outstation Hinxton, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK).

This application was modified for inclusion in EMBOSS by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

Completed 22nd March 1999.

## Target users

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

## Comments