Alignment of optical maps

Anton Valouev, Lei Li, Yu Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman

Research output: Contribution to journalConference article

1 Citation (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)489-504
Number of pages16
JournalLecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)
Volume3500
StatePublished - Oct 17 2005
Event9th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2005 - Cambridge, MA, United States
Duration: May 14 2005May 18 2005

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Alignment
Likelihood Ratio
Scoring
Residual Plots
Error Model
Bernoulli
Siméon Denis Poisson
Framework
False

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Valouev, A., Li, L., Liu, Y. C., Schwartz, D. C., Yang, Y., Zhang, Y., & Waterman, M. S. (2005). Alignment of optical maps. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science), 3500, 489-504.
Valouev, Anton ; Li, Lei ; Liu, Yu Chi ; Schwartz, David C. ; Yang, Yi ; Zhang, Yu ; Waterman, Michael S. / Alignment of optical maps. In: Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 2005 ; Vol. 3500. pp. 489-504.
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Valouev, A, Li, L, Liu, YC, Schwartz, DC, Yang, Y, Zhang, Y & Waterman, MS 2005, 'Alignment of optical maps', Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science), vol. 3500, pp. 489-504.

Alignment of optical maps. / Valouev, Anton; Li, Lei; Liu, Yu Chi; Schwartz, David C.; Yang, Yi; Zhang, Yu; Waterman, Michael S.

In: Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science), Vol. 3500, 17.10.2005, p. 489-504.

Research output: Contribution to journalConference article

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AU - Valouev, Anton

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AU - Liu, Yu Chi

AU - Schwartz, David C.

AU - Yang, Yi

AU - Zhang, Yu

AU - Waterman, Michael S.

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AB - 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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Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y et al. Alignment of optical maps. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 2005 Oct 17;3500:489-504.