DDmap: a MATLAB package for the double digest problem using multiple genetic operators

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.

[1]  Gerhard J. Woeginger,et al.  Double Digest Revisited: Complexity and Approximability in the Presence of Noisy Data , 2003, COCOON.

[2]  Ming-Yang Kao,et al.  The Enhanced Double Digest Problem for DNA Physical Mapping , 2003, J. Comb. Optim..

[3]  Mark Stefik,et al.  Inferring DNA Structures from Segmentation Data , 1978, Artif. Intell..

[4]  H. Smith,et al.  A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. , 1970, Journal of molecular biology.

[5]  Pavel A. Pevzner.  DNA Physical Mapping, Flows in Networks and Minimum Cycles Mean in Graphs , 1992, Mathematical Methods Of Analysis Of Biopolymer Sequences.

[6]  Y. Zhang,et al.  Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear programming , 2008, Int. J. Bioinform. Res. Appl..

[7]  M. Waterman,et al.  Multiple solutions of DNA restriction mapping problems , 1991 .

[8]  Jerrold R. Griggs,et al.  Interval graphs and maps of DNA. , 1986, Bulletin of mathematical biology.

[9]  H. Smith,et al.  Restriction endonucleases in the analysis and restructuring of dna molecules. , 1975, Annual review of biochemistry.

[10]  Pavel A. Pevzner,et al.  DNA physical mapping and alternating Eulerian cycles in colored graphs , 1995, Algorithmica.

[11]  Richard M. Karp,et al.  Mapping the genome: some combinatorial problems arising in molecular biology , 1993, STOC.

[12]  M. Waterman,et al.  Mapping DNA by stochastic relaxation , 1987 .

[13]  Mohammad Ganjtabesh,et al.  Genetic algorithm solution for double digest problem , 2012, Bioinformation.

[14]  Edmund K. Burke,et al.  On the complexity of the Double Digest Problem , 2004 .

[15]  C. A. Murthy,et al.  Genetic Algorithm for Double Digest Problem , 2005, PReMI.