                                newcpgreport



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Function

   Identify CpG islands in nucleotide sequence(s)

Description

   newcpgreport 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 used to
   identify regions which match the 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.

Algorithm

   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
   Cs in the window multiplied by the number of Gs 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 newcpgreport


% newcpgreport
Identify CpG islands in nucleotide sequence(s)
Input nucleotide sequence(s): tembl:u68037
Window size [100]:
Shift increment [1]:
Minimum Length [200]:
Minimum observed/expected [0.6]:
Minimum percentage [50.]:
Output file [u68037.newcpgreport]:


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

Command line arguments

Identify CpG islands in nucleotide sequence(s)
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -window             integer    [100] Window size (Integer 1 or more)
   -shift              integer    [1] Shift increment (Integer 1 or more)
   -minlen             integer    [200] Minimum Length (Integer 1 or more)
   -minoe              float      [0.6] Minimum observed/expected (Number from
                                  0.000 to 10.000)
   -minpc              float      [50.] Minimum percentage (Number from 0.000
                                  to 100.000)
  [-outfile]           outfile    [*.newcpgreport] Output file name

   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
   -scircular1         boolean    Sequence is circular
   -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

   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

   newcpgreport reads one or more nucleic acid sequences.

  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

  Output files for usage example

  File: u68037.newcpgreport

ID   U68037  1218 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       104..509
FT                    /size=406
FT                    /Sum C+G=269
FT                    /Percent CG=66.26
FT                    /ObsExp=0.81
FT   CpG island       596..924
FT                    /size=329
FT                    /Sum C+G=223
FT                    /Percent CG=67.78
FT                    /ObsExp=1.01
FT   numislands       2
//

Data files

   None.

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.

   newcpgreport is used in the production of the CpG Island database
   'CPGISLE'. It produces a report for potential CpG islands in CPGISLE
   database entry format. See the FTP site:
   ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the finished database.

   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

    1. Larsen F., Gundersen, G., Lopez L., Prydz H. "CpG island as Gene
       Markers in the Human Genome" Genomics 13:1095-1107 (1992)

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description
   cpgplot          Identify and plot CpG islands in nucleotide sequence(s)
   cpgreport        Identify and report CpG-rich regions in nucleotide
                    sequence(s)
   geecee           Calculate fractional GC content of nucleic acid sequences
   newcpgseek       Identify and report CpG-rich regions in nucleotide
                    sequence(s)

Author(s)

   Rodrigo Lopez
   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

   Written (1999) - Rodrigo Lopez.

Target users

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

Comments

   None
