
                                 cpgreport 



Function

   Reports all CpG rich regions

Description

   cpgreport scans a nucleotide sequence for regions with higher than
   expected frequencies of the dinucleotide CG.

   CpG refers to a C nucleotide immediately followed by a G. The 'p' in
   'CpG' refers to the phosphate group linking the two bases.

   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.

   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". cpgreport 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.

   This method overpredicts islands but finds the smaller ones around
   primary exons.

Usage

   Here is a sample session with cpgreport


% cpgreport tembl:rnu68037 
Reports all CpG rich regions
CpG score [17]: 
Output file [rnu68037.cpgreport]: 
Output features [rnu68037.gff]: 

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
   -score              integer    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.
  [-outfile]           outfile    Output file name
  [-outfeat]           featout    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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -score 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 17
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.cpgreport
   [-outfeat]
   (Parameter 3) File for output features Writeable feature table
   unknown.gff
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   Any DNA sequence USA.

  Input files for usage example

   'tembl:rnu68037' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:rnu68037

ID   RNU68037   standard; RNA; ROD; 1218 BP.
XX
AC   U68037;
XX
SV   U68037.1
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; Rodentia; Sciurognathi; 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
DR   SWISS-PROT; P70597; PE21_RAT.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /db_xref="taxon:10116"
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P70597"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /product="EP1 prostanoid receptor"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFS
M
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTA
G
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALAL
L
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAAL
V
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALR
S
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLA
V
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSR
H
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        6
0
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       12
0
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       18
0
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       24
0
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       30
0
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       36
0
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       42
0
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       48
0
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       54
0
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       60
0
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       66
0
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       72
0
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       78
0
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       84
0
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       90
0
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       96
0
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      102
0
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      108
0
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      114
0
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      120
0
     ggcttcagcc acttgtga                                                    121
8
//

Output file format

  Output files for usage example

  File: rnu68037.cpgreport



CPGREPORT of RNU68037 from 1 to 1218

Sequence              Begin    End Score        CpG   %CG  CG/GC
RNU68037                 12     13    17          1 100.0    -
RNU68037                 47     48    17          1 100.0    -
RNU68037                 96   1032   630         87  66.1   0.65
RNU68037               1072   1100    26          3  62.1   0.00
RNU68037               1139   1140    17          1 100.0    -
RNU68037               1183   1193    26          2  72.7   2.00

  File: rnu68037.gff

##gff-version 2.0
##date 2004-07-15
##Type DNA RNU68037
RNU68037        cpgreport       misc_feature    12      13      17.000  +
.       Sequence "RNU68037.1"
RNU68037        cpgreport       misc_feature    47      48      17.000  +
.       Sequence "RNU68037.2"
RNU68037        cpgreport       misc_feature    96      1032    630.000 +
.       Sequence "RNU68037.3"
RNU68037        cpgreport       misc_feature    1072    1100    26.000  +
.       Sequence "RNU68037.4"
RNU68037        cpgreport       misc_feature    1139    1140    17.000  +
.       Sequence "RNU68037.5"
RNU68037        cpgreport       misc_feature    1183    1193    26.000  +
.       Sequence "RNU68037.6"

   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.

   The second non-blank line contains the headings of the columns.

   Subsequent lines contain columns with the following information:

     * The name of the sequence.
     * The begin position and the end position of the CpG-rich region.
     * The score of the CpG-rich region.
     * The number of CpG's in the CpG-rich region.
     * The %(G+C) in the CpG-rich region.
     * The ratio of CpG to GpC in the CpG-rich region.

   If the count of GpC in the region is zero, then the ratio of CG/GC is
   reported as '-'.

Data files

   None.

Notes

   This program does not find CpG islands as normally defined (see
   cpgplot).

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   0 if successful.

Known bugs

   None.

See also

   Program name                          Description
   cpgplot      Plot CpG rich areas
   geecee       Calculates the fractional GC content of nucleic acid sequences
   newcpgreport Report CpG rich areas
   newcpgseek   Reports CpG rich regions

   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)

   This program was originally written by Gos Micklem (gos © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

   The algorithm was modified for inclusion in EGCG under the name
   'CPGSPANS' by Rodrigo Lopez (rls © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   This application was modified for inclusion in EMBOSS by Alan Bleasby
   (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Completed 22nd March 1999.

Target users

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

Comments

   None
