Fast analysis of highly repetitive sequences in human chromosomes using a novel search algorithm

Abstrae!: We have developed an algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences and it is fast enough as to be used at a genomic scale running on a standard personal computer. In this study, we apply our algorithm to compare the composition of Alu highly repetitive sequences in two human chromosomes, namely chromosomes 21 and 22, each of them about 33 million nucleotides-long. We show that our method allows th\.iquantification and comparison of hundreds of thousands of Alu sequences in a few minutes. We determine that both human chromosomes have different numbers and types of Alu sequences, in agreement with previous data. We also observe that DNA methylation has a profound impact on Alu sequence conservation. Future applications of this method are discussed.