Detecting localized interspersed motifs in genomic sequences

Repeated sequences account for a significant fraction of Eukaryotic genomes - nearly half of the human genome consists of repeated sequence elements. Several elements have been linked to diseases. Consequently, identifying and characterizing repeated elements is essential for understanding diseases at the molecular level. Repeated sequences vary from one genome to another and are therefore difficult to identify using sequence comparison methods alone. Certain gene families, such as the interferon gene family or the natural killer gene complex, have been found to be clustered together in the genome. Several observations have lead to the hypothesis that specific sequence repeats could be playing an important role in generating multigene families. Here, we define the concept of localized interspersed motifs and present a computational approach for detecting them.