A Progressive Strategy for DNA Resequencing Problem

In this paper, we are going to solve the DNA resequencing problem. We are given a set of subseuqences obtained by the next generation sequencing (NGS) technology and we are asked to assembly them into a DNA sequence with the aid of a reference sequence. In this paper, we propose a progressive strategy to solve the resequencing problem. Our algorithm allows us to map data to reference sequence efficiently. Compared with other available tools, our approach allows us to be able to map much more subsequences to the reference sequence. 1 A Brief Introduction of the String Matching Problems As we shall see later, the DNA resequencing problem is a variation of the traditional string matching problems. Therefore, a brief introduction of the string matching problems and notations often used will be first given below. In string matching problems, there are a text n and a pattern m where both ’s and i ’s are characters. We assume that . We denote j i i by and j i i by . We shall consider two different kinds of string matching problems: Exact string matching problem and approximate string matching problems. t t t T L 2 1 = p p p P L 2 1 = i t p n m ≤ t t t L 1 + ) , ( j i T p p p L 1 + ) , ( j i P For the exact string matching problem, we are given a text n and a pattern m . Our job is to find whether t t t T L 2 1 =