A Novel Algorithm for Finding Interspersed Repeat Regions

• Published in: Genomics, proteomics & bioinformatics Vol. 2; no. 3; pp. 184 - 191
• Main Authors: Li, Dongdong, Wang, Zhengzhi, Ni, Qingshan
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.08.2004; College of Mechatronics Engineering and Automation, National University of Defense Technology, Changsha 410073, China; Elsevier
• Subjects: Algorithms; assemble; Computational Biology - methods; Escherichia coli - genetics; Evaluation Studies as Topic; Genomics - methods; Interspersed Repetitive Sequences - genetics; Letter; random projection; repeats; assemble; repeats; random projection
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/S1672-0229(04)02024-8

The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together. The complexity of our projection-assemble algorithm is nearly linear to the length of the genome sequence, and its memory usage is limited by the hardware. We tested our algorithm with both simulated data and real biology data, and the results show that our projection-assemble algorithm is efficient. By means of this algorithm, we found an un-labeled repeat region that occurs five times in Escherichia coli genome, with its length more than 5,000bp, and a mismatch probability less than 4%.