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We present three heuristics - Sliding Window, Look Ahead, and Iterative Sliding Window - to improve solutions for the Sorting Signed Permutations by Reversals and Transpositions Problem. We investigate the classical version of the problem as well as versions restricted to prefix and prefix or suffix operations. To assess the heuristics based on its improvement, we implemented algorithms described in the literature to provide initial solutions. Although we have a limited number of problems, these heuristics can be applied to many others within the area of genome rearrangement. When time is a crucial factor, Sliding Window is a better choice because it runs in linear time. If the quality of the solution is a priority, Look Ahead should be preferred. Iterative Sliding Window is the most flexible heuristic and allows us to find a trade-off for specific scenarios where running time and solution quality are relevant.
This article was published in the following journal.
Name: IEEE/ACM transactions on computational biology and bioinformatics
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Trial-and-error methods of problem-solving used when an algorithmic approach is impractical
Experience-based techniques for problem-solving, learning, and discovery that find a solution which is not guaranteed to be optimal, but sufficient for a given set of goals.
Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
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The act of knowing or the recognition of a distance by recollective thought, or by means of a sensory process which is under the influence of set and of prior experience.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...