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cpgplot

cpgplot

cpgplot is a tool for plotting and identification of CpG islands in nucleotide sequences. The cpgplot algorithm computes CpG islands in overlapping windows along a sequence and by default defines a CpG island where the percent G + C is more than 50% and the observed vs. expected ratio is over 0.6. The minimum length of the region is 200 bases and at least 10 windows.

Topic

Sequence composition, complexity and repeats

Details

  • Operation: CpG island and isochore detection
  • Software interface: Command-line user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: emboss _at_ emboss.open-bio.org;emboss _at_ emboss.open-bio.org;emboss-bug _at_ emboss.open-bio.org
  • Collection: EMBOSS

Publications

Rice P, Longden I, Bleasby A "EMBOSS: the European Molecular Biology Open Software Suite." Trends Genet. 2000; 16(6):276-7 https://doi.org/10.1016/s0168-9525(00)02024-2
PMID: 10827456


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