Takai Daiya, Jones Peter A
Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, USA.
In Silico Biol. 2003;3(3):235-40.
Clusters of CpG dinucleotides in GC rich regions of the genome called "CpG islands" frequently occur in the 5' ends of genes. Methylation of CpG islands plays a role in transcriptional silencing in higher organisms in certain situations. We have established a CpG-island-extraction algorithm, which we previously developed [Takai and Jones, 2002], on a web site which has a simple user interface to identify CpG islands from submitted sequences of up to 50kb. The web site determines the locations of CpG islands using parameters (lower limit of %GC, ObsCpG/ExpCpG, length) set by the user, to display the value of parameters on each CpG island, and provides a graphical map of CpG dinucleotide distribution and borders of CpG islands. A command-line version of the CpG islands searcher has also been developed for larger sequences. The CpG Island Searcher was applied to the latest sequence and mapping information of human chromosomes 20, 21 and 22, and a total of 2345 CpG islands were extracted and 534 (23%) of them contained first coding exons and 650 (28%) contained other exons. The CpG Island Searcher is available on the World Wide Web at http://www.cpgislands.com or http://www.uscnorris.com/cpgislands/cpg.cgi.
基因组富含GC区域中被称为“CpG岛”的CpG二核苷酸簇经常出现在基因的5'端。在某些情况下，CpG岛的甲基化在高等生物的转录沉默中起作用。我们在一个具有简单用户界面的网站上建立了一种CpG岛提取算法，该算法是我们之前开发的[Takai和Jones，2002]，用于从提交的长达50kb的序列中识别CpG岛。该网站使用用户设置的参数（%GC下限、ObsCpG/ExpCpG、长度）来确定CpG岛的位置，以显示每个CpG岛上的参数值，并提供CpG二核苷酸分布和CpG岛边界的图形化图谱。还开发了用于处理更大序列的命令行版本的CpG岛搜索工具。CpG岛搜索工具应用于人类20号、21号和22号染色体的最新序列和图谱信息，共提取了2345个CpG岛，其中534个（23%）包含首个编码外显子，650个（28%）包含其他外显子。CpG岛搜索工具可通过万维网在http://www.cpgislands.com或http://www.uscnorris.com/cpgislands/cpg.cgi上获取。
