Alignment of Optical Maps

  • Anton Valouev
  • Lei Li
  • Yu-Chi Liu
  • David C. Schwartz
  • Yi Yang
  • Yu Zhang
  • Michael S. Waterman
Conference paper

DOI: 10.1007/11415770_37

Volume 3500 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Valouev A. et al. (2005) Alignment of Optical Maps. In: Miyano S., Mesirov J., Kasif S., Istrail S., Pevzner P.A., Waterman M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science, vol 3500. Springer, Berlin, Heidelberg

Abstract

We introduce a new scoring method for calculation of alignments of optical maps. Missing cuts, false cuts and sizing errors present in optical maps are addressed by our alignment score through calculation of corresponding likelihood ratios. The Sizing error model is derived through the application of CLT and validated by residual plots collected from real data. Missing cuts and false cuts are modeled as Bernoulli and Poisson events respectively. This probabilistic framework is used to derive an alignment score through calculation of likelihood ratio. Consequently, this allows to achieve maximal descriminative power for alignment calculation. The proposed scoring method is naturally embedded within a well known DP framework for finding optimal alignments.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Anton Valouev
    • 1
  • Lei Li
    • 1
  • Yu-Chi Liu
    • 2
  • David C. Schwartz
    • 4
  • Yi Yang
    • 1
  • Yu Zhang
    • 3
  • Michael S. Waterman
    • 1
  1. 1.Department of MathematicsUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.Molecular and Computational Biology Program, Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesUSA
  3. 3.Department of StatisticsHarvard UniversityCambridgeUSA
  4. 4.Laboratory for Molecular and Computational Genomics, Departments of Genetics and ChemistryUniversity of Wisconsin-MadisonMadisonUSA