EMBOSS: newcpgseek

| ## EMBOSS: newcpgseek

# Program newcpgseek

## Function

Reports CpG rich regions

## Description

newcpgseek reports CpG rich regions of a sequence as candidate CpG islands.

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 finds regions where there is a high absolute frequency of CpG dimers as well as a high proportion of CpG compared to GpC.

## Usage

Here is a sample session with newcpgseek.

    % newcpgseek
    Input sequence: embl:rnu68037
    CpG score [17]:
    Output file [rnu68037.newcpgseek]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -score              integer    CpG score
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       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 | CpG score | Integer from 1 to 200 | 17
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.newcpgseek
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

A nucleic acid sequence.

## Output file format

Here is the output from the example run:

    NEWCPGSEEK of RNU68037 from 1 to 1218
    with score > 17

     Begin    End  Score        CpG  %CG  CG/GC
    *    96   1032   630         87  66.1   0.65
      1072   1100    26          3  62.1   0.00
      1183   1193    26          2  72.7   2.00
    -------------------------------------------

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

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

## Author(s)

This application was written by Rodrigo Lopez (rls@ebi.ac.uk) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

## History

Written (1999) - Rodrigo Lopez

## Target users

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

## Comments