|   | newcpgseek | 
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.
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!
Non-mammalian vertebrates have some CpG islands that are associated with genes, but the association gets equivocal in the farther taxonomic groups.
Finding a CpG island upstream of predicted exons or genes is good contributory evidence.
CpG islands are usually defined as "length over 200bp with %GC over 50% and obs/ervedexpexted CpG more than 0.6". However this program uses a running sum rather than a window to produce a score: if there is not a CpG at position i, then decrement runSum counter, but if CpG then runSum += CPGSCORE. Spans above the threshold are searched for recursively. If the score is higher than a threshold (17 at the moment) then a putative island is declared.
This program reads in one or more sequences and finds regions where there is a high absolute frequency of CpG dimers as well as a high proportion of CpG compared to GpC.
| % newcpgseek Reports CpG rich regions Input nucleotide sequence(s): tembl:u68037 CpG score [17]: Output file [u68037.newcpgseek]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -score              integer    [17] CpG score (Integer from 1 to 200)
  [-outfile]           outfile    [*.newcpgseek] 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
   -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
   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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -score | CpG score | Integer from 1 to 200 | 17 | 
| [-outfile] (Parameter 2) | Output file name | Output file | <*>.newcpgseek | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 
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
//
 | 
| NEWCPGSEEK of U68037 from 1 to 1218 with score > 17 Begin End Score CpG %CG CG/GC * 96 1032 630 87 66.1 0.65 1072 1100 26 3 62.1 0.00 1183 1193 26 2 72.7 2.00 ------------------------------------------- | 
| Program name | Description | 
|---|---|
| cpgplot | Plot CpG rich areas | 
| cpgreport | Reports all CpG rich regions | 
| geecee | Calculates fractional GC content of nucleic acid sequences | 
| newcpgreport | Report CpG rich areas | 
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.