A fast exact sequential algorithm for the partial digest problem.

Mostafa M Abbas,Hazem M Bahig

doi:10.1186/s12859-016-1365-2

Mostafa M Abbas, Hazem M Bahig

Open Access

https://doi.org/10.1186/s12859-016-1365-2

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Abstract

BackgroundRestriction 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.ResultsIn 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.ConclusionOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1365-2) contains supplementary material, which is available to authorized users.

Highlights

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
Test methodology we present the methodology that is used to evaluate the performance of the algorithms, BBd, BBb and BBb2, according to their running times and memory consumptions
In the BBb algorithm, we built the solution tree for the PDP in the breadth-first manner instead of the depth-first manner taking into consideration two conditions of pruning and deleting all repeated subproblems in the same level

Summary

Introduction

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. 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. The restriction enzymes are used to cut a DNA molecule at restriction sites with the goal of identifying the locations of the restriction sites after digestion. Their positions in the genome are determined by analyzing the lengths of the digested DNA. Based on the experimental assumptions of digestion, there are two main

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Conclusion