Joint base-calling of Two DNA Sequences with Factor Graphs
Name
Shi-2010-Joint base-calling of Two DNA Sequences with Factor Graphs.pdf
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Author(s)
Shi, Xiaomeng
Lun, Desmond S.
Medard, Muriel
Koetter, Ralf
Meldrim, James C.
Barry, Andrew James
Date Issued
February 2010
Journal
IEEE transactions on information theory
Publisher
Institute of Electrical and Electronics Engineers
Citation
Lun, D.S. et al., with Xiaomeng Shi. “Joint Base-Calling of Two DNA Sequences With Factor Graphs.” Information Theory, IEEE Transactions On 56.2 (2010) : 724-733. Copyright © 2010, IEEE
Version
Final published version
Abstract
Automated estimation of DNA base-sequences is an important step in genomics and in many other emerging fields in biological and medical sciences. Current automated sequencers process single strands only. To improve the utility of existing technologies, we propose to mix two independent strands prior to electrophoresis, and base-call jointly by applying the sum-product algorithm on factor graphs. We first present a statistical model for DNA sequencing data and examine the model parameters. A practical heuristic is then proposed to estimate the peaks, which are then separated into two source sequences (Major/Minor) by passing messages on a factor graph. Simulation results show that joint base-calling can provide less accurate but valid results for the minor. The algorithm presented provides a basis for future investigation of joint sequencing techniques.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1109/TIT.2009.2037029
