Genomics Inform.  2010 Mar;8(1):58-61.

CpG Islands Detector: a Window-based CpG Island Search Tool

Affiliations
  • 1Department of Biomedical Technology, Sangmyung University, Cheonan 330-720, Korea. kbkim@smu.ac.kr

Abstract

CpG is the pair of nucleotides C and G, appearing successively, in this order, along one DNA strand. It is known that due to biochemical considerations CpG is relatively rare in most DNA sequences. However, in particular subsequences, which are a few hundred to a few thousand nucleotides long, the couple CpG is more frequent. These subsequences, called CpG islands, are known to appear in biologically more significant parts of the genome. The ability to identify CpG islands along a chromosome will therefore help us spot its more significant regions of interest, such as the promoters or 'start' regions of many genes. In this respect, I developed the CpG islands search tool, CpG Islands Detector, which was implemented in JAVA to be run on any platform. The window-based graphical user interface of CpG Islands Detector may facilitate the end user to employ this tool to pinpoint CpG islands in a genomic DNA sequence. In addition, this tool can be used to highlight potential genes in genomic sequences since CpG islands are very often found in the 5' regions of vertebrate genes.

Keyword

CpG island; promoter; CpG islands detector; JAVA; graphical user interface

MeSH Terms

Base Sequence
CpG Islands
DNA
Genome
Indonesia
Nucleotides
Vertebrates
DNA
Nucleotides
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