See the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the finished database.
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 for that gene's existance.
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.
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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 display 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 the method which mentioned in the Description section above. 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 useful for detecting sequences that MIGHT contain an island.