EMBOSS: newcpgreport

| ## EMBOSS: newcpgreport

# Program newcpgreport

## Function

Report CpG rich areas

## Description

This application is used in the production of the CpG Island database 'CPGISLE'. It produces CPGISLE database entry format reports for a potential CpG island.

See the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the finished database.

## Usage

Here is a sample session with newcpgreport.

    % newcpgreport
    Input sequence: embl:rnu68037
    Window size [100]:
    Shift increment [1]:
    Minimum Length [200]:
    Minimum observed/expected [0.6]:
    Minimum percentage [50.]:
    Output file [rnu68037.newcpgreport]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -window             integer    Window size
       -shift              integer    Shift increment
       -minlen             integer    Minimum Length
       -minoe              float      Minimum observed/expected
       -minpc              float      Minimum percentage
      [-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
-window | Window size | Integer 1 or more | 100
-shift | Shift increment | Integer 1 or more | 1
-minlen | Minimum Length | Integer 1 or more | 200
-minoe | Minimum observed/expected | Number from 0.000 to 10.000 | 0.6
-minpc | Minimum percentage | Number from 0.000 to 100.000 | 50.
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.newcpgreport
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

One or more nucleic acid sequences.

## Output file format

Here is the output file from the example run:

    ID   RNU68037  1118 BP.
    XX
    DE   CpG Island report.
    XX
    CC   Obs/Exp ratio > 0.60.
    CC   % C + % G > 50.00.
    CC   Length > 200.
    XX
    FH   Key              Location/Qualifiers
    FT   CpG island       157..389
    FT                    /size=232
    FT                    /Sum C+G=152
    FT                    /Percent CG=65.24
    FT                    /ObsExp=0.73
    FT   CpG island       654..963
    FT                    /size=309
    FT                    /Sum C+G=206
    FT                    /Percent CG=66.45
    FT                    /ObsExp=0.96
    FT   numislands       2
    //

## Data files

None.

## Notes

None.

## References

1. Larsen F., Gundersen, G., Lopez L., Prydz H. CpG island as Gene Markers in the Human Genome Genomics 13:1095-1107 (1992)

## 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
newcpgseek | Reports CpG rich regions

## 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