DNA Sequencing via Quantum Mechanics and Machine Learning

Details DNA Sequencing via Quantum Mechanics and Machine Learning DNA Sequencing via Quantum Mechanics and Machine Learning

2010-12-04

arxiv.org/abs/1012.0900v1

International Journal of Computational Science, Vol. 4, No. 4, 2010. pp. 352 - 370

Physics

Biological Physics

19 pages, 7 figures

Scientific paper

Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for rapid DNA sequencing, but unfortunately the tunneling current alone cannot distinguish the four nucleotides due to large fluctuations in molecular conformation and solvent. Here, we propose a machine-learning approach applied to the tunneling current-voltage (I-V) characteristic for efficient discrimination between the four nucleotides. We first combine principal component analysis (PCA) and fuzzy c-means (FCM) clustering to learn the "fingerprints" of the electronic density-of-states (DOS) of the four nucleotides, which can be derived from the I-V data. We then apply the hidden Markov model and the Viterbi algorithm to sequence a time series of DOS data (i.e., to solve the sequencing problem). Numerical experiments show that the PCA-FCM approach can classify unlabeled DOS data with 91% accuracy. Furthermore, the classification is found to be robust against moderate levels of noise, i.e., 70% accuracy is retained with a signal-to-noise ratio of 26 dB. The PCA-FCM-Viterbi approach provides a 4-fold increase in accuracy for the sequencing problem compared with PCA alone. In conjunction with recent developments in nanotechnology, this machine-learning method may pave the way to the much-awaited rapid, low-cost genome sequencer.

Affiliated with

Also associated with

No associations

Rating

DNA Sequencing via Quantum Mechanics and Machine Learning does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with DNA Sequencing via Quantum Mechanics and Machine Learning, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA Sequencing via Quantum Mechanics and Machine Learning will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-99294