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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="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>
<p>
<H2>
Function
</H2>
Plot CpG rich areas
<H2>
Description
</H2>
CpG refers to a C nucleotide immediately followed by a G. The 'p' in
'CpG' refers to the phosphate group linking the two bases.
<p>
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.
<p>
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!
<p>
Non-mammalian vertebrates have some CpG islands that are associated with
genes, but the association gets equivocal in the farther taxonomic
groups.
<p>
Finding a CpG island upstream of predicted exons or genes is good
contributory evidence.
<p>
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.
<p>
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'.
<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>
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with cpgplot</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cpgplot tembl:u68037 -graph cps </b>
Plot CpG rich areas
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>
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 postition 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,
tekt, tek, none, data, xterm, png, gif)
[-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
-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
-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 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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</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>
<td>-window</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 postition that the window is moved to.</td>
<td>Integer 1 or more</td>
<td>100</td>
</tr>
<tr>
<td>-minlen</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>
<td>-minoe</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>
<td>-minpc</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>
<td>[-outfile]<br>(Parameter 2)</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><*></i>.cpgplot</td>
</tr>
<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr>
<td>[-outfeat]<br>(Parameter 3)</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=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-[no]plot</td>
<td>Plot CpG island score</td>
<td>Toggle value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-[no]obsexp</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>
<td>-[no]cg</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>
<td>-[no]pc</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>
</table>
<H2>
Input file format
</H2>
Any DNA sequence USA.
<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 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
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="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>
<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 > 0.60
Percent C + Percent G > 50.00
Length > 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 2.0
##date 2006-07-15
##Type DNA U68037
U68037 cpgplot misc_feature 104 509 0.000 + . Sequence "U68037.1"
U68037 cpgplot misc_feature 596 924 0.000 + . Sequence "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>
None.
<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>Reports all CpG rich regions</td>
</tr>
<tr>
<td><a href="geecee.html">geecee</a></td>
<td>Calculates fractional GC content of nucleic acid sequences</td>
</tr>
<tr>
<td><a href="newcpgreport.html">newcpgreport</a></td>
<td>Report CpG rich areas</td>
</tr>
<tr>
<td><a href="newcpgseek.html">newcpgseek</a></td>
<td>Reports CpG rich regions</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)
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Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Completed 23rd March 1999.
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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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