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 journalArticlepeer-review

65 Scopus citations


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 likelihoods. The size error model is derived through the application of Central Limit Theorem and validated by residual plots collected from real data. Missing cuts and false cuts are modeled as Bernoulli and Poisson events, respectively, as suggested by previous studies. Likelihoods are used to derive an alignment score through calculation of likelihood ratios for a certain hypothesis test. This allows us to achieve maximal descriminative power for the alignment score. Our scoring method is naturally embedded within a well known DP framework for finding optimal alignments.

Original languageEnglish (US)
Pages (from-to)442-462
Number of pages21
JournalJournal of Computational Biology
Issue number2
StatePublished - Mar 2006

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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