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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.
By default, this program defines a CpG island as a region where, over an average of 10 windows, the calculated % composition is over 50% and the calculated Obs/Exp ratio is over 0.6 and the conditions hold for a minimum of 200 bases. These conditions can be modified by setting the values of the appropriate parameters.
The Expected number of CpG patterns 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.
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 Input sequence: embl:rnu68037 CpG score [17]: Output file [rnu68037.newcpgseek]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -score integer CpG score [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-score | CpG score | Integer from 1 to 200 | 17 |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.newcpgseek |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
NEWCPGSEEK of RNU68037 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 the fractional GC content of nucleic acid sequences |
newcpgreport | Report CpG rich areas |