An Efficient Algorithm for Finding Highly Conserved Regulatory Elements among Orthologous DNA Sequences

Abstract

In current genome research, the identification of regulatory elements required for the correct expression of genes is an essential topic. FootPrinter (Blanchette, 2000; Blanchette and Tompa, 2003) is a well established tool for identifying regulatory elements from a set of orthologous non-coding DNA sequences of various species under a given phylogenetic tree. Such a motif/substring finding problem has been defined as the substring parsimony problem by Blanchette (2000). We design a new algorithm which adopts the hashing technique and a fast approach to detect the Hamming distance between two substings to resolve this problem. Experimental results show that our approach is more efficient than FootPrinter when the substrings needed are highly conserved.