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Maximum likelihood DNA sequence detection via sphere decoding

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2 Author(s)
Ting Wu ; Department of Electrical and Computer Engineering, The University of Texas, Austin, USA ; Vikalo, H.

In sequencing-by-synthesis systems, determining the order of nucleotides of a DNA fragment can be cast as an ML sequence detection (MLSD) problem. Solving it via exhaustive search is prohibitive even for relatively short DNA sequences. Symbol-by-symbol and partial-MLSD solutions are computationally feasible but sacrifice the optimal performance. In this paper, we modify the so-called sphere decoding algorithm to efficiently solve the MLSD problem in sequencing-by-synthesis systems. We analyze the expected complexity of the algorithm, and demonstrate via simulations that it significantly outperforms heuristic techniques.

Published in:

Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on

Date of Conference:

14-19 March 2010