
                             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
