Classification of Promoter Sequences from Human Genome

We have developed a new method for promoter sequence classification based on a genetic algorithm and the MAHDS sequence alignment method. We have created four classes of human promoters, combining 17,310 sequences out of the 29,598 present in the EPD database. We searched the human genome for potential promoter sequences (PPSs) using dynamic programming and position weight matrices representing each of the promoter sequence classes. A total of 3,065,317 potential promoter sequences were found. Only 1,241,206 of them were located in unannotated parts of the human genome. Every other PPS found intersected with either true promoters, transposable elements, or interspersed repeats. We found a strong intersection between PPSs and Alu elements as well as transcript start sites. The number of false positive PPSs is estimated to be 3 x 10(-8) per nucleotide, which is several orders of magnitude lower than for any other promoter prediction method. The developed method can be used to search for PPSs in various eukaryotic genomes.

Automated summary

We have developed a new method for classifying promoter sequences using a genetic algorithm and the MAHDS sequence alignment method. Four classes of human promoters were created, using 17,310 sequences from the EPD database. A search for potential promoter sequences (PPSs) in the human genome was conducted, resulting in 3,065,317 PPSs, with only 1,241,206 located in unannotated regions. Intersections were found between PPSs and true promoters, transposable elements, and interspersed repeats.