Alignment of optical maps

Authors:
Anton Valouev;Lei Li;Yu-Chi Liu;David C. Schwartz;Yi Yang;Yu Zhang;Michael S. Waterman
Affiliations:
Department of Mathematics, University of Southern California, Los Angeles, CA;Department of Mathematics, University of Southern California, Los Angeles, CA;Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA;Laboratory for Molecular and Computational Genomics, Departments of Genetics and Chemistry, University of Wisconsin-Madison, Madison, WI;Department of Mathematics, University of Southern California, Los Angeles, CA;Department of Statistics, Harvard University, Cambridge, MA;Department of Mathematics, University of Southern California, Los Angeles, CA
Venue:
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Year:
2005

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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.