A Fast Exact Repeats Search Algorithm for Genome Analysis

The repeat structure of genomic DNA is considered an essential mechanism for evolution and other fundamental biological functions. Repeats finding problems are always deemed as one of the prerequisites for genome sequencing and analysis, and among these problems exact repeat finding is the first step for most other repeats finding problems. In this paper, the authors propose a new fast algorithm based on simple count sort and radix sort to solve the exact repeat finding problems specifically, which performs more efficient than any existing exact repeat finding algorithm by the simplicity of data structure and the proposed algorithm itself. The algorithm can also be easily adapted for similar problems in proteome sequence analysis with little modification.