|   | cpgreport | 
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cpgreport identifies in a nucleotide sequence regions with higher than expected frequency of the dinucleotide CG.
Each position in the sequence is scored using a running sum calculated from all positions in the sequence. This is a different method to that typically used for identifying CpG islands, for example by newcpgreport and cpgplot. This method overpredicts islands but finds the smaller ones around primary exons. An output file is written with information on the CpG-rich regions that are found. A feature table of sequence features in these regions is also written.cpgreport scores each position in the sequence using a running sum calculated from all positions in the sequence, starting with the first and ending in the last. 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.
| % cpgreport tembl:u68037 Identify and report CpG-rich regions in nucleotide sequence(s) CpG score [17]: Output file [u68037.cpgreport]: Features output [u68037.gff]: | 
Go to the input files for this example
Go to the output files for this example
| 
Identify and report CpG-rich regions in nucleotide sequence(s)
Version: EMBOSS:6.6.0.0
   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
   -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
   "-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
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| -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. | Integer from 1 to 200 | 17 | 
| [-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.cpgreport | 
| [-outfeat] (Parameter 3) | featout | File for output features | Writeable feature table | unknown.gff | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0 | 
| -send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0 | 
| -sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N | 
| -sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | 
| -snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N | 
| -sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N | 
| -slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N | 
| -supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N | 
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | 
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | 
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | 
| -sdbname1 -sdbname_sequence | string | Database name | Any string | |
| -sid1 -sid_sequence | string | Entryname | Any string | |
| -ufo1 -ufo_sequence | string | UFO features | Any string | |
| -fformat1 -fformat_sequence | string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence | string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| "-outfeat" associated featout qualifiers | ||||
| -offormat3 -offormat_outfeat | string | Output feature format | Any string | |
| -ofopenfile3 -ofopenfile_outfeat | string | Features file name | Any string | |
| -ofextension3 -ofextension_outfeat | string | File name extension | Any string | |
| -ofdirectory3 -ofdirectory_outfeat | string | Output directory | Any string | |
| -ofname3 -ofname_outfeat | string | Base file name | Any string | |
| -ofsingle3 -ofsingle_outfeat | boolean | Separate file for each entry | Boolean value Yes/No | N | 
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
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.
| 
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
//
 | 
| 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 | 
| ##gff-version 3 ##sequence-region U68037 1 1193 #!Date 2013-07-15 #!Type DNA #!Source-version EMBOSS 6.6.0.0 U68037 cpgreport sequence_feature 12 13 17 + . ID=U68037.1 U68037 cpgreport sequence_feature 47 48 17 + . ID=U68037.2 U68037 cpgreport sequence_feature 96 1032 630 + . ID=U68037.3 U68037 cpgreport sequence_feature 1072 1100 26 + . ID=U68037.4 U68037 cpgreport sequence_feature 1139 1140 17 + . ID=U68037.5 U68037 cpgreport sequence_feature 1183 1193 26 + . ID=U68037.6 | 
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:
If the count of GpC in the region is zero, then the ratio of CG/GC is reported as '-'.
"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.
| Program name | Description | 
|---|---|
| cpgplot | Identify and plot CpG islands 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) | 
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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
The algorithm was modified for inclusion in EGCG under the name 'CPGSPANS' by
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 © emboss.open-bio.org) not to the original author.
This application was modified for inclusion in EMBOSS by 
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 © emboss.open-bio.org) not to the original author.