Algorithms and Design for an Autonomous Biological System

Various global rearrangements of permutations, such as reversals and transpositions, have recently become of interest because of their applications in computational molecular biology, to be more specific, genome rearrangement. Many primitives have been formulated in this regard. These primitives find their applications hugely in the study of the similarity of different organisms. In this paper, we formulate a new primitive for genome rearrangement, the strip exchanges. An approximation algorithm for the strip exchanges problem with an approximation guarantee of 2.66 has been designed. We present this algorithm along with its mathematical analysis. We propose the design of an autonomous biological system which detects the similarity of different species by matching their genomes. We use the primitive strip exchanges to match two genomes in our system. A comparison of the other existing primitives with strip exchanges has been given. Various other pragmatic applications of such a system have also been touched upon.