                                   cpgplot



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Function

   Identify and plot CpG islands in nucleotide sequence(s)

Description

   cpgplot 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.

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

   By default, cpgplot 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.

   The Observed number of CpG patterns in a window is simply 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

Usage

   Here is a sample session with cpgplot


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

Created cpgplot.ps


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

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


Input file format

   cpgplot reads one or more nucleotide sequences.

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

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

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

   The input format can be specified by using the command-line qualifier
   -sformat xxx, 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.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

   'tembl:u68037' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:u68037

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 & 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
//

Output file format

   The output is to the specified graphics device.

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

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

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

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

   See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
   information on supported devices.

  Output files for usage example

  File: u68037.cpgplot



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)

  File: u68037.gff

##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

  Graphics File: cpgplot.ps

   [cpgplot results]

Notes

   "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.

   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:

   1. cpgplot and newcpgreport 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:
   Observed/Expected ratio > 0.6
   % C + % G > 50%
   Sequence Length > 200

   2. newcpgseek and cpgreport use a running sum calculated from all
   positions in a sequence rather than a window to produce a score. If
   there is not a CG 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.

   This method 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. For most purposes you should
   probably use newcpgreport rather than cpgreport. 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.

   newcpgseek and cpgreport 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.

   The geecee 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 might contain an island.

References

   The original program was described in:
    1. 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        Identify and report CpG-rich regions in nucleotide
                    sequence(s)
   geecee           Calculate fractional GC content of nucleic acid sequences
   newcpgreport     Identify CpG islands in nucleotide sequence(s)
   newcpgseek       Identify and report CpG-rich regions in nucleotide
                    sequence(s)

   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
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None
