Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the lengths of the cut DNA. Using different reaction times with a single enzyme to cut DNA is a technique known as a partial digestion. Determining the exact locations of restriction sites following a partial digestion is challenging due to the computational time required even with the best known practical algorithm. In this paper, we introduce an efficient algorithm to find the exact solution for the partial digest problem. The algorithm is able to find all possible solutions for the input and works by traversing the solution tree with a breadth-first search in two stages and deleting all repeated subproblems. Two types of simulated data, random and Zhang, are used to measure the efficiency of the algorithm. We also apply the algorithm to real data for the Luciferase gene and the E. coli K12 genome. Our algorithm is a fast tool to find the exact solution for the partial digest problem. The percentage of improvement is more than 75% over the best known practical algorithm for the worst case. For large numbers of inputs, our algorithm is able to solve the problem in a suitable time, while the best known practical algorithm is unable.

The RSA (Rivest–Shamir–Adleman) asymmetric-key cryptosystem is widely used for encryptions and digital signatures. Let $(n,e)$ be the RSA public key and d be the corresponding private key (or private exponent). One of the attacks on RSA is to find the private key d using continued fractions when d is small. In this paper, we present a new technique to improve a small private exponent attack on RSA using continued fractions and multicore systems. The idea of the proposed technique is to find an interval that contains $\varphi \left(n\right),$ and then propose a method to generate different points in the interval that can be used by continued fraction and multicore systems to recover the private key, where $\varphi$ is Euler’s totient function. The practical results of three small private exponent attacks on RSA show that we extended the previous bound of the private key that is discovered by continued fractions. When n is 1024 bits, we used 20 cores to extend the bound of d by $0.016$ for de Weger, Maitra-Sarkar, and Nassr et al. attacks in average times 7.67 h, 2.7 h, and 44 min, respectively.