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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: cpgplot
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
cpgplot
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Identify and plot CpG islands in nucleotide sequence(s)
<H2>
    Description
</H2>

<p><b>cpgplot</b> identifies CpG islands in one or more nucleotide sequences. The ratio of observered to expected number of GC dinucleotides patterns is calculated over a window (sequence region) which is moved along the sequence. The calculated ratios are plotted graphically, together with the regions which match this program's definition of a "CpG island" (a CG dinucleotide rich area).  A report file is written giving the input sequence name, CpG island parameters and data on any CpG islands that are found.</p>

<!-- Algorithm -->
<p>The ratio of observered to expected number of GC dinucleotides patterns is calculated over a window of user-specified size (<tt>-window</tt> parameter).  The window is slid along the sequence and the ratio recalculated until the end of the sequence is reached.</p>

<p>By default, <b>cpgplot</b> defines a CpG island as a region where, over an average of 10 windows and not less than 200 bases, the calculated (%G + %C) content is over 50% and the calculated Observed/Expected ratio is over 0.6. These conditions can be modified by setting the values of the appropriate parameters.</p>

<p>The Observed number of CpG patterns in a window is simply the number of times a 'C' is found followed immediately by a 'G'.</p>

<p>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.</p>

<pre>Expected = (number of C's  * number of G's) / window length</pre>



<H2>
    Usage
</H2>
Here is a sample session with <b>cpgplot</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>cpgplot tembl:u68037 -graph cps </b>
Identify and plot CpG islands in nucleotide sequence(s)
Window size [100]: <b></b>
Minimum length of an island [200]: <b></b>
Minimum observed/expected [0.6]: <b></b>
Minimum percentage [50.]: <b></b>
Output file [u68037.cpgplot]: <b></b>
Features output [u68037.gff]: <b></b>

Created cpgplot.ps

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Identify and plot CpG islands in nucleotide sequence(s)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -window             integer    [100] 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 position that the window is moved
                                  to. (Integer 1 or more)
   -minlen             integer    [200] This sets the minimum length that a
                                  CpG island has to be before it is reported.
                                  (Integer 1 or more)
   -minoe              float      [0.6] 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)
   -minpc              float      [50.] 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)
  [-outfile]           outfile    [*.cpgplot] 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    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)
  [-outfeat]           featout    [unknown.gff] File for output features

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]plot           toggle     [Y] Plot CpG island score
   -[no]obsexp         boolean    [Y] 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    [Y] 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    [Y] 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfeat" associated qualifiers
   -offormat3          string     Output feature format
   -ofopenfile3        string     Features file name
   -ofextension3       string     File name extension
   -ofdirectory3       string     Output directory
   -ofname3            string     Base file name
   -ofsingle3          boolean    Separate file for each entry

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-window</td>
<td>integer</td>
<td>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 position that the window is moved to.</td>
<td>Integer 1 or more</td>
<td>100</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-minlen</td>
<td>integer</td>
<td>This sets the minimum length that a CpG island has to be before it is reported.</td>
<td>Integer 1 or more</td>
<td>200</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-minoe</td>
<td>float</td>
<td>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.</td>
<td>Number from 0.000 to 10.000</td>
<td>0.6</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-minpc</td>
<td>float</td>
<td>This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported.</td>
<td>Number from 0.000 to 100.000</td>
<td>50.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>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.</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.cpgplot</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-graph</td>
<td>xygraph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfeat]<br>(Parameter 3)</td>
<td>featout</td>
<td>File for output features</td>
<td>Writeable feature table</td>
<td><i>unknown.gff</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]plot</td>
<td>toggle</td>
<td>Plot CpG island score</td>
<td>Toggle value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]obsexp</td>
<td>boolean</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]cg</td>
<td>boolean</td>
<td>If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]pc</td>
<td>boolean</td>
<td>If this is set to true then the graph of the percentage C plus G within a window is displayed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqall qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-graph" associated xygraph qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gprompt</td>
<td>boolean</td>
<td>Graph prompting</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdesc</td>
<td>string</td>
<td>Graph description</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gtitle</td>
<td>string</td>
<td>Graph title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gsubtitle</td>
<td>string</td>
<td>Graph subtitle</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gxtitle</td>
<td>string</td>
<td>Graph x axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gytitle</td>
<td>string</td>
<td>Graph y axis title</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -goutfile</td>
<td>string</td>
<td>Output file for non interactive displays</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -gdirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfeat" associated featout qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -offormat3<br>-offormat_outfeat</td>
<td>string</td>
<td>Output feature format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofopenfile3<br>-ofopenfile_outfeat</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofextension3<br>-ofextension_outfeat</td>
<td>string</td>
<td>File name extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofdirectory3<br>-ofdirectory_outfeat</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofname3<br>-ofname_outfeat</td>
<td>string</td>
<td>Base file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ofsingle3<br>-ofsingle_outfeat</td>
<td>boolean</td>
<td>Separate file for each entry</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>

<b>cpgplot</b> reads one or more nucleotide sequences.
<p>
<p>

The input is a standard EMBOSS sequence query (also known as a 'USA').

<p>
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

<p>

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

<p>
The input format can be specified by using the
command-line qualifier <tt>-sformat xxx</tt>, where 'xxx' is replaced
by the name of the required format.  The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

<p>

See:
<A href="http://emboss.sf.net/docs/themes/SequenceFormats.html">
http://emboss.sf.net/docs/themes/SequenceFormats.html</A>
for further information on sequence formats.

<p>

<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tembl:u68037' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:u68037</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP.
XX
AC   U68037;
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; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   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 INSDC.
RL   Biochemistry &amp; Molecular Biology, Merck Frosst Center for Therapeutic
RL   Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
DR   Ensembl-GO; ENSRNOESTG00000830631; Rattus_norvegicus.
DR   Ensembl-Gn; ENSRNOG00000004094; Rattus_norvegicus.
DR   Ensembl-Gn; ENSRNOG00000017743; Rattus_norvegicus.
DR   Ensembl-TO; ENSRNOESTT00000830623; Rattus_norvegicus.
DR   Ensembl-Tr; ENSRNOT00000005470; Rattus_norvegicus.
DR   Ensembl-Tr; ENSRNOT00000023860; Rattus_norvegicus.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:10116"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /product="EP1 prostanoid receptor"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /db_xref="GOA:P70597"
FT                   /db_xref="InterPro:IPR000276"
FT                   /db_xref="InterPro:IPR000708"
FT                   /db_xref="InterPro:IPR001244"
FT                   /db_xref="InterPro:IPR008365"
FT                   /db_xref="InterPro:IPR017452"
FT                   /db_xref="UniProtKB/Swiss-Prot:P70597"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        60
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       120
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       180
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       240
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       300
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       360
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       420
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       480
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       540
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       600
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       660
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       720
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       780
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       840
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       900
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       960
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      1020
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      1080
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      1140
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      1200
     ggcttcagcc acttgtga                                                    1218
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>

<p>

The output is to the specified graphics device.

<p>

The results can be output in one of several formats by using the
command-line qualifier <b>-graph xxx</b>, where 'xxx' is replaced by
the name of the required device. Support depends on the availability
of third-party software packages.

<p>
The device names that output to a file are:
ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470,
hp7580, das, data.

<p> The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.

<p>
Output can be turned off by specifying none (null).

<p>

See:
<A href="http://emboss.sf.net/docs/themes/GraphicsDevices.html">
http://emboss.sf.net/docs/themes/GraphicsDevices.html</A>
for further information on supported devices.

<p>

<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: u68037.cpgplot</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>


CPGPLOT islands of unusual CG composition
U68037 from 1 to 1218

     Observed/Expected ratio &gt; 0.60
     Percent C + Percent G &gt; 50.00
     Length &gt; 200

 Length 406 (104..509)

 Length 329 (596..924)
</pre>
</td></tr></table><p>
<p><h3>File: u68037.gff</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
##gff-version 3
##sequence-region U68037 1 924
#!Date 2013-07-15
#!Type DNA
#!Source-version EMBOSS 6.6.0.0
U68037	cpgplot	sequence_feature	104	509	.	+	.	ID=U68037.1
U68037	cpgplot	sequence_feature	596	924	.	+	.	ID=U68037.2
</pre>
</td></tr></table><p>
<p><h3>Graphics File: cpgplot.ps</h3>
<p><img src="cpgplot.1.cpgplot.gif" alt="[cpgplot results]">


<H2>
    Notes
</H2>

<p>"CpG" refers to a C nucleotide immediately followed by a G. The 'p' in 'CpG' refers to the phosphate group linking the two bases. Regions of genomic sequences rich in the CpG pattern or "CpG islands" are resistant to methylation and tend to be associated with genes which are frequently switched on. It's been estimated that about half of all mammalian genes, and, possibly all mammalian house-keeping genes, have a CpG-rich region around their 5' end.  Non-mammalian vertebrates have some CpG islands that are associated with genes, but the association gets equivocal in the farther taxonomic groups. The detection of CpG island upstream of predicted exons or genes is evidence in support of a highly expressed gene.</p>


<p>As there is no official definition of what is a CpG island is or how to identify where they begin and end, we work with two definitions and thus two methods. These are:</p>

<p>1. <b>cpgplot</b> and <b>newcpgreport</b> use a sliding window within which the Observed/Expected ratio of CpG is calculated. For a sequence region to reported as a CpG island, it must satisfy the following contraints:</p>
<pre>
   Observed/Expected ratio > 0.6
   % C + % G > 50%
   Sequence Length > 200
</pre>

<p>2. <b>newcpgseek</b> and <b>cpgreport</b> use a running sum calculated from all positions in a sequence rather than a window to produce a score.  If there is not a <tt>CG</tt> dinucleotide at a position, the score is decremented, if there is one, the score is incremented by a constant (user-defined) value. If the score for a region in the sequence is higher than a threshold (17 at the moment) then a putative island is declared.  Sequence regions scoring above the threshold are searched for recursively.</p> 

<p>This method overpredicts islands but finds the smaller ones around primary exons. <b>newcpgseek</b> uses the same method as <b>cpgreport</b> but the output is different and more readable. For most purposes you should probably use <b>newcpgreport</b> rather than <b>cpgreport</b>. It is 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.</p>
<p><b>newcpgseek</b> and <b>cpgreport</b> both now display the actual CpG count, the (%C + %G) and the Observed/Expected ratio in the region where the score is above the threshold.</p>
<p>The <b>geecee</b> program measures CG content in the entire input sequence and is not to be used to detect CpG islands. It can be useful for detecting sequences that <em>might</em> contain an island.</p>


<H2>
    References
</H2>

The original program was described in:

<ol>

<li>
Larsen F, Gundersen G, Lopez R, Prydz H
"CpG islands as gene markers in the human genome."
Genomics 1992 Aug;13(4):1095-107

</ol>

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

    0 if successful.

<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="cpgreport.html">cpgreport</a></td>
<td>Identify and report CpG-rich regions in nucleotide sequence(s)</td>
</tr>

<tr>
<td><a href="geecee.html">geecee</a></td>
<td>Calculate fractional GC content of nucleic acid sequences</td>
</tr>

<tr>
<td><a href="newcpgreport.html">newcpgreport</a></td>
<td>Identify CpG islands in nucleotide sequence(s)</td>
</tr>

<tr>
<td><a href="newcpgseek.html">newcpgseek</a></td>
<td>Identify and report CpG-rich regions in nucleotide sequence(s)</td>
</tr>

</table>


<p>

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:

<p>

1.  <b>newcpgseek</b> and <b>cpgreport</b> - 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.
<b>newcpgseek</b> uses the same method as <b>cpgreport</b> but the
output is different and more readable.

<p>

2.  <b>newcpgreport</b> and <b>cpgplot</b> 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:

<p>
<pre>
   Obs/Exp ratio > 0.6
   % C + % G > 50%
   Length > 200.
</pre>
<p>

<p>

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.

<p>

<b>geecee</b> 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.
        

<H2>
    Author(s)
</H2>
Alan Bleasby 
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>

Completed 23rd March 1999.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

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</HTML>