Detection of repetitive nucleotides in DNA sequences

摘要

Numerous repetitive elements are found in abundance in genomes. Many applications of molecular genetic approaches, such as the DNA fingerprinting for identifying an individual, are related to the repetitive elements. Increasing the number of repetitive elements has been implicated in several genetic diseases. Recognition of the repetitive elements is an important issue in genomic analysis. A computational method for detecting repeated nucleotides in DNA sequences with no prior knowledge of the patterns is proposed. Searching the repeat was approached by similar pattern matching. A table of nucleotide patterns was built by sliding a window across the DNA sequence. The table holds, for each pattern, all the positions where the pattern is located in the sequence. Based on the list of indexes, the region candidate is drawn from the sequence. The best alignment of the candidate and the DNA sequence extends both ends of the region, resulting in the repeat. The algorithm exhibited a good selectivity in detecting nucleotide repeats in five human genes. Although it is not the most efficient method for searching the repetitive nucleotides in DNA sequences, the algorithm can easily be implemented.