MIT Libraries logoDSpace@MIT

MIT
View Item 
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

Joint base-calling of Two DNA Sequences with Factor Graphs

Author(s)
Shi, Xiaomeng; Lun, Desmond S.; Medard, Muriel; Koetter, Ralf; Meldrim, James C.; Barry, Andrew James; ... Show more Show less
Thumbnail
DownloadShi-2010-Joint base-calling of Two DNA Sequences with Factor Graphs.pdf (248.7Kb)
PUBLISHER_POLICY

Publisher Policy

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.

Terms of use
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.
Metadata
Show full item record
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.
Date issued
2010-02
URI
http://hdl.handle.net/1721.1/62009
Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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
Other identifiers
INSPEC Accession Number: 11152616
ISSN
0018-9448

Collections
  • MIT Open Access Articles

Browse

All of DSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

My Account

Login

Statistics

OA StatisticsStatistics by CountryStatistics by Department
MIT Libraries
PrivacyPermissionsAccessibilityContact us
MIT
Content created by the MIT Libraries, CC BY-NC unless otherwise noted. Notify us about copyright concerns.