Algorithms for optimizing production DNA sequencing

We discuss the problem of optimally "finishing" a partially sequenced, reconstructed DNA segment. At first sight, this appears to be computationally hard. We construct a series of increasingly realistic models for the problem and show that all of these can in fact be solved to optimality in polynomial time, with near-optimal solutions available in linear time. Implementation of our algorithms could result in a substantial efficiency gain for automated DNA sequencing.

• Type: Conference
• Year: 2000
• Where: SODA
• Authors: Éva Czabarka, Goran Konjevod, Madhav V. Marathe, Allon G. Percus, David C. Torney
• Keywords: Algorithms, DNA Segment, Realistic Models, SODA 2000, Substantial Efficiency Gain