Heath Samuel A, Preparata Franco P, Young Joel
Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912-1910, USA.
J Comput Biol. 2003;10(3-4):499-508. doi: 10.1089/10665270360688147.
DNA sequencing by hybridization, potentially a powerful alternative to standard wet lab techniques, has received renewed interest after a novel probing scheme has been recently proposed whose performance for the first time asymptotically meets the information theory bound. After settlement of the question of asymptotic performance, there remains the issue of algorithmic fine tunings aimed at improving the performance "constants," with substantial practical implications. In this paper, we show that a probing scheme based on the joint use of direct and reverse spectra (tandem spectra) for a given gapped probing pattern achieves a performance improvement per unit of microarray area of about 5/4 and does not appear to be susceptible to further improvement by increasing the number of cooperating spectra. In other words, tandem-spectrum reconstruction is the best known technique for sequencing by hybridization.
