Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case.
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, and the elasticity parameters of the unzipped strands.
Baldazzi
V
V
Dipartimento di Fisica, Università di Roma Tor Vergata, Roma, Italy.
Bradde
S
S
Cocco
S
S
Marinari
E
E
Monasson
R
R
D000465:Algorithms; D001483:Base Sequence; D001499:Bayes Theorem; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D019277:Entropy; D015233:Models, Statistical; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011336:Probability; D013816:Thermodynamics; D013997:Time Factors
D004247:DNA