
                                  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 (i.e. Observed/Expected) 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 Observed number of CpG patterns in a window is simply the count of
   the number of times a 'C' is found followed immediately by a 'G'.
   
   The Expected number of CpG patterns is calculated for each window as
   the number of CpG dinucleotides you would expect to see in that window
   based on the frequency of C's and G's in that window. Thus, the
   Expected frequency of CpG's 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.
   
        Expected = (number of C's  * number of G's) / 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 tembl:rnu68037 -graph cps 
Plot CpG rich areas
Window size [100]: 
Window shift increment [1]: 
Minimum length of an island [200]: 
Minimum observed/expected [0.6]: 
Minimum percentage [50.]: 
Output file [rnu68037.cpgplot]: 
Output features [rnu68037.gff]: 

Created cpgplot.ps
   
   Go to the input files for this example
   Go to the output files for this example
   
Command line arguments

   Standard (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
  [-outfeat]           featout    File for output features

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]obsexp         boolean    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             boolean    If this is set to true then the graph of the
                                  regions which have been determined to be
                                  CpG islands is displayed.
   -[no]pc             boolean    If this is set to true then the graph of the
                                  percentage C plus G within a window is
                                  displayed.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -odirectory2         string     Output directory

   "-graph" associated qualifiers
   -gprompt3            boolean    Graph prompting
   -gtitle3             string     Graph title
   -gsubtitle3          string     Graph subtitle
   -gxtitle3            string     Graph x axis title
   -gytitle3            string     Graph y axis title
   -goutfile3           string     Output file for non interactive displays
   -gdirectory3         string     Output directory

   "-outfeat" associated qualifiers
   -offormat4           string     Output feature format
   -ofopenfile4         string     Features file name
   -ofextension4        string     File name extension
   -ofdirectory4        string     Output directory
   -ofname4             string     Base file name
   -ofsingle4           boolean    Separate file for each entry

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths
   

   Standard (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
   [-outfeat]
   (Parameter 4) File for output features Writeable feature table
   unknown.gff
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) 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.
   Boolean value 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. Boolean value
   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. Boolean value Yes/No Yes
   
Input file format

   Any DNA sequence USA.
   
  Input files for usage example
  
   'tembl:rnu68037' is a sequence entry in the example nucleic acid
   database 'tembl'
   
  Database entry: tembl:rnu68037
  
ID   RNU68037   standard; RNA; ROD; 1218 BP.
XX
AC   U68037;
XX
SV   U68037.1
XX
DT   23-SEP-1996 (Rel. 49, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE   Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds.
XX
KW   .
XX
OS   Rattus norvegicus (Norway rat)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   "Cloning of the rat EP1 prostanoid receptor";
RL   Unpublished.
XX
RN   [2]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   ;
RL   Submitted (26-AUG-1996) to the EMBL/GenBank/DDBJ databases.
RL   Biochemistry & Molecular Biology, Merck Frosst Center for Therapeutic
RL   Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
DR   SWISS-PROT; P70597; PE21_RAT.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /db_xref="taxon:10116"
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P70597"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /product="EP1 prostanoid receptor"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFS
M
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTA
G
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALAL
L
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAAL
V
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALR
S
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLA
V
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSR
H
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        6
0
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       12
0
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       18
0
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       24
0
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       30
0
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       36
0
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       42
0
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       48
0
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       54
0
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       60
0
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       66
0
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       72
0
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       78
0
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       84
0
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       90
0
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       96
0
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      102
0
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      108
0
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      114
0
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      120
0
     ggcttcagcc acttgtga                                                    121
8
//
   
Output file format

  Output files for usage example
  
  Graphics File: cpgplot.ps
  
   [cpgplot results]
   
  File: rnu68037.cpgplot
  


CPGPLOT islands of unusual CG composition
RNU68037 from 1 to 1218

     Observed/Expected ratio > 0.60
     Percent C + Percent G > 50.00
     Length > 200

 Length 406 (104..509)

 Length 329 (596..924)
   
  File: rnu68037.gff
  
##gff-version 2.0
##date 2004-04-06
##Type DNA RNU68037
RNU68037        cpgplot misc_feature    104     509     0.000   +       .
Sequence "RNU68037.1"
RNU68037        cpgplot misc_feature    596     924     0.000   +       .
Sequence "RNU68037.2"
   
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
   
   As there is no official definition of what is a cpg island is, and
   worst where they begin and end, we have to live with 2 definitions and
   thus two methods. These are:
   
   1. newcpgseek and cpgreport - both declare a putative island if the
   score is higher than a threshold (17 at the moment). They now also
   displaying the actual CpG count, the % CG and the observed/expected
   ration in the region where the score is above the threshold. This
   scoring method based on sum/frequencies overpredicts islands but finds
   the smaller ones around primary exons. newcpgseek uses the same method
   as cpgreport but the output is different and more readable.
   
   2. newcpgreport and cpgplot use a sliding window within which the
   Obs/Exp ratio of CpG is calculated. The important thing to note in
   this method is that an island, in order to be reported, is defined as
   a region that satisfies the following contraints:
   
   Obs/Exp ratio > 0.6
   % C + % G > 50%
   Length > 200.

   For all practical purposes you should probably use newcpgreport. It is
   actually used to produce the human cpgisland database you can find on
   the EBI's ftp server as well as on the EBI's SRS server.
   
   geecee measures CG content in the entire input sequence and is not to
   be used to detect CpG islands. It can be usefull for detecting
   sequences that MIGHT contain an island.
   
Author(s)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
   
History

Completed 23rd March 1999.

Target users

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