Method for predicting regulatory elements in repetitive sequences using transcription factor binding sites

摘要

Repeat sequences are the most abundant in the extragenic region of genomes, while a large number of regulatory elements are found in this region. The invention attempts to mine rules on how combinations of individual binding sites are distributed in repeat sequences. These mined association rules would facilitate identifying gene classes regulated by similar mechanisms and accurately predicting regulatory elements. Herein, the combinations of transcription factor binding sites in the repeat sequences are obtained, and data mining techniques are applied to mine the association rules from the combinations of binding sites. In addition, the associations are further pruned to remove insignificant associations and obtain a set of discovered associations. The discovered association rules are used to partially classify the repeat sequences in the repeat sequence database.