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© 1998 Cold Spring Harbor Laboratory
CpG Promoter2 is software developed by Drs. Ilya Ioshikhes and. Michael Zhang at Cold Spring Harbor Laboratory (CSHL) for large-scale promoter mapping using CpG islands. CpG islands are defined as exceeding 200 bp, having more than 50% C+G content and a CpG frequency at least 0.6 of that expected on the basis of C+G content of the region. Approximately half of the mammalian gene promoters are associated with one or more CpG islands. CpG Promoter is based on a quadratic discrimination analysis between promoter-associated CpG islands and non-associated ones. It enables an efficient mapping of promoters with 2Kb resolution, if there is a CpG island inside an interval (-500…+1500) around a transcription start site (TSS). It correctly mapped approximately 93% of the promoters containing CpG islands.
CSHL is making CorePromoter and CpG Promoter site licenses available to commercial entities for internal use for a one-time fee of $5,000 each. If both programs are licensed together, however, the total Promoter Software package is $8,000. Reference 3 describes the use of these two programs in tandem.
Zhang M.Q. "Identification of Human Gene Core-Promoters in Silico", Genome Res 1998 Mar; 8(3):319-26.
Ioshikhes I.P. & Zhang M.Q. "Large-scale human promoter mapping using CpG islands", Nature Genetics (2000) Sept.; 26:61-63.
Zhang M.Q. "Discriminant analysis and its application in DNA sequence motif recognition", Briefings in Bioinformatics (2000); 1(4):331-342.
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