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© 1998 Cold Spring Harbor Laboratory
CorePromoter1 is software developed by Dr. Michael Zhang at Cold Spring Harbor Laboratory (CSHL) that predicts putative Transcriptional Start Sites (TSS) in genomic sequences ranging from 250 to 2000 bp, and hence defines the core-promoter within this extended promoter interval. Identification of the 5’-end of human genes from genome sequence data has been difficult because of the hierarchical and modular nature of promoter architecture. While other methods employ neural networks or search for transcription factor sites, CorePromoter is based on a quadratic discrimination analysis of human core-promoters. In statistical tests this software was able to localize a TSS to a 100 bp interval about 60% of the time.
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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