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<HTML>
<HEAD>
<TITLE>
EMBOSS: cpgreport
</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">
cpgreport
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Reports all CpG rich regions
<H2>
Description
</H2>
<b>cpgreport</b> scans a nucleotide sequence for regions with higher than
expected frequencies of the dinucleotide CG.
<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.
<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>
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". <b>cpgreport</b> 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.
<p>
This method overpredicts islands but finds the smaller ones around
primary exons.
<H2>
Usage
</H2>
<b>Here is a sample session with cpgreport</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cpgreport tembl:u68037 </b>
Reports all CpG rich regions
CpG score [17]: <b></b>
Output file [u68037.cpgreport]: <b></b>
Features output [u68037.gff]: <b></b>
</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:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-score integer [17] 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)
[-outfile] outfile [*.cpgreport] Output file name
[-outfeat] featout [unknown.gff] File for output features
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
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
"-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>-score</td>
<td>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.</td>
<td>Integer from 1 to 200</td>
<td>17</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.cpgreport</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 colspan=4>(none)</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.cpgreport</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
CPGREPORT of U68037 from 1 to 1218
Sequence Begin End Score CpG %CG CG/GC
U68037 12 13 17 1 100.0 -
U68037 47 48 17 1 100.0 -
U68037 96 1032 630 87 66.1 0.65
U68037 1072 1100 26 3 62.1 0.00
U68037 1139 1140 17 1 100.0 -
U68037 1183 1193 26 2 72.7 2.00
</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 cpgreport misc_feature 12 13 17.000 + . Sequence "U68037.1"
U68037 cpgreport misc_feature 47 48 17.000 + . Sequence "U68037.2"
U68037 cpgreport misc_feature 96 1032 630.000 + . Sequence "U68037.3"
U68037 cpgreport misc_feature 1072 1100 26.000 + . Sequence "U68037.4"
U68037 cpgreport misc_feature 1139 1140 17.000 + . Sequence "U68037.5"
U68037 cpgreport misc_feature 1183 1193 26.000 + . Sequence "U68037.6"
</pre>
</td></tr></table><p>
<p>
The first non-blank line of the output file 'rnu68037.cpgreport' is the
title line giving the program name, the name of sequence being analysed
and the start and end positions of the sequence.
<p>
The second non-blank line contains the headings of the columns.
<p>
Subsequent lines contain columns with the following information:
<p>
<ul>
<li>The name of the sequence.
<li>The begin position and the end position of the CpG-rich region.
<li>The score of the CpG-rich region.
<li>The number of CpG's in the CpG-rich region.
<li>The %(G+C) in the CpG-rich region.
<li>The ratio of CpG to GpC in the CpG-rich region.
</ul>
<p>
If the count of GpC in the region is zero, then the ratio of CG/GC is
reported as '-'.
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
This program does not find CpG islands as normally defined (see cpgplot).
<H2>
References
</H2>
None.
<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="cpgplot.html">cpgplot</a></td>
<td>Plot CpG rich areas</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>
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>
This program was originally written by
Gos Micklem (gos © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
The algorithm was modified for inclusion in EGCG under the name 'CPGSPANS' by
Rodrigo Lopez (rls © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
This application was modified for inclusion in EMBOSS by
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Completed 22nd 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>
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