CorePromoter is a Transcriptional Start Site (TSS) prediction program based on a Quadratic Discrimination Analysis of human core-promoters. The input genomic DNA sequence (larger than 240 bp and less than 2,001 bp) is assumed to contain a functional core-promoter (-60,+40) with respect to the TSS (+1) (see: Zhang M.Q. "Identification of Human Gene Core-Promters in Silico", to appear in the Bioinformatics special issue of Genome Research, March, 1998.) Our statistical test showed that CorePromoter was able to localize a TSS to a 100-bp interval ~60% of the time (measured by the highest peak of the scoring profile falling within (-50,+50) of the true TSS).

Parameters:

(1) Strand -- If the Crick strand is chosen, coordinate will be enumerated reversely.
(2) Prior Probability -- How likely can a TSS be found by chance.
(3) QDA data -- LEDB uses QDA covariant matrix trained by 673 human promoter sequences built from our non-redundant Lead Exon Database; EPD uses QDA covariant matrix trained by 177 non-redundant human promoter sequences built from EPD48.
(4) Maximum number -- Maximum number of predictions sorted by the profile scores.

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-Michael Zhang
Mar. 3, 1998; Apr.9, 1998.
Cold Spring Harbor Laboratiry

* CorePromoter (c) 1998 Cold Spring Harbor Laboratory" is available for free to non-profit institutions using it for non-commercial purposes. Commercial users may obtain a site license for a fee. For information about obtaining a commercial use license contact Dr. Carol Dempster, email: dempster@cshl.org, Phone: 516-367-6885 or Fax: 516-367-8855. ALL RIGHTS RESERVED.

REFERENCE:Zhang M.Q. (1998) "Identification of Human Gene Core-Promters in Silico", to appear in the Bioinformatics special issue of Genome Research.

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