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Global alignment of molecular sequences via ancestral state reconstruction

Author

Listed:
  • Andoni, Alexandr
  • Daskalakis, Constantinos
  • Hassidim, Avinatan
  • Roch, Sebastien

Abstract

We consider the trace reconstruction problem on a tree (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves. The TRPT is motivated by the multiple sequence alignment problem in computational biology. We give a simple recursive procedure giving strong reconstruction guarantees at low mutation rates. To our knowledge, this is the first rigorous trace reconstruction result on a tree in the presence of indels.

Suggested Citation

  • Andoni, Alexandr & Daskalakis, Constantinos & Hassidim, Avinatan & Roch, Sebastien, 2012. "Global alignment of molecular sequences via ancestral state reconstruction," Stochastic Processes and their Applications, Elsevier, vol. 122(12), pages 3852-3874.
  • Handle: RePEc:eee:spapps:v:122:y:2012:i:12:p:3852-3874
    DOI: 10.1016/j.spa.2012.08.004
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