PRELIMINARY ABSTRACT:
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Constraints and Global Optimization for Gene Prediction Overlap Resolution 
Christian Theil Have
Keywords: 
gene prediction, overlap resolution, constraints, global optimization, probabilistic model, Constraint Handling Rules, PRISM
Abstract: 
We apply constraints and global optimization to the problem of restricting
overlapping of gene predictions for prokaryotic genomes.
We investigate existing heuristic methods and show how they may be
expressed using Constraint Handling Rules.  Furthermore, we integrate existing
methods with a global optimization procedure expressed as probabilistic model
in the PRISM language.  The approach has comparable accuracy to the heuristic
approaches, but can provide optimality guarantees with regard to final set of predictions.