Multiplex dispensation order generation for pyrosequencing

Abstract

This paper introduces the multiplex dispensation order generation problem, a real-life combinatorial problem that arises in the context of analyzing large numbers of short to medium length DNA sequences. The problem is modeled as a constraint optimization problem (COP). We present the COP, its constraint programming formulation, and a custom search procedure. We give some experimental data supporting our design decisions. One of the lessons learnt from this study is that the ease with which the relevant constraints are expressed can be a crucial factor in making design decisions in the COP model.