Abstract
BackgroundIn computational biology, the physical mapping of DNA is a key problem. We know that the double digest problem (DDP) is NP-complete. Many algorithms have been proposed for solving the DDP, although it is still far from being resolved.ResultsWe present DDmap, an open-source MATLAB package for solving the DDP, based on a newly designed genetic algorithm that combines six genetic operators in searching for optimal solutions. We test the performance of DDmap by using a typical DDP dataset, and we depict exact solutions to these DDP instances in an explicit manner. In addition, we propose an approximate method for solving some hard DDP scenarios via a scaling-rounding-adjusting process.ConclusionsFor typical DDP test instances, DDmap finds exact solutions within approximately 1 s. Based on our simulations on 1000 random DDP instances by using DDmap, we find that the maximum length of the combining fragments has observable effects towards genetic algorithms for solving the DDP problem. In addition, a Maple source code for illustrating DDP solutions as nested pie charts is also included.
Highlights
In computational biology, the physical mapping of DNA is a key problem
The physical mapping of DNA is a key problem in computational biology [5]
To test the utility of DDmap, eight double digest problem (DDP) instances, referred to as INSj(j = 1⋯8), are taken from [13]. They are shown in the following Table 2: First, the integrated effects of the six aforementioned genetic operators of DDmap are verified
Summary
We know that the double digest problem (DDP) is NP-complete. The physical mapping of DNA is a key problem in computational biology [5]. A large DNA molecule is a long string composed of four nucleotides, A, C, G and T. Double digest experiments (DDE for short) are a standard approach for constructing physical DNA maps [2]. We obtain three multisets of short DNA fragments. Due to certain experimental limitations, only the length information (i.e., The number of nucleotides) of these short fragments can be measured with certain accuracy using certain mature biological techniques, such as gel
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