A statistical model for unwarping of 1-D

C.A. Glasbey, L. Vali, J. Gustafsson

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

A statistical model is proposed which relates density profiles in 1-D electrophoresis gels, such as those produced by pulsed-field gel electrophoresis (PFGE), to databases of profiles of known genotypes. The warp in each gel lane is described by a trend that is linear in its parameters plus a first-order autoregressive process, and density differences are modelled by a mixture of two normal distributions. Maximum likelihood estimates are computed efficiently by a recursive algorithm that alternates between dynamic time warping to align individual lanes and generalised-least-squares regression to ensure that the warp is smooth between lanes. The method, illustrated using PFGE of Escherichia coli O157 strains, automatically unwarps and classifies gel lanes, and facilitates manual identification of new genotypes
Original languageEnglish
Pages (from-to)4327-4242
Number of pages6
JournalElectrophoresis
Volume26
Issue number22
DOIs
Publication statusPublished - 2005

    Fingerprint

Keywords

  • autoregressive process
  • Pulsed-field gel electrophoresis
  • mixture distribution
  • image warping
  • dynamic programming

Cite this

Glasbey, C. A., Vali, L., & Gustafsson, J. (2005). A statistical model for unwarping of 1-D. Electrophoresis, 26(22), 4327-4242. https://doi.org/10.1002/elps.200500365