Global alignment of molecular sequences via ancestral state reconstruction

Alexandr Andoni; Constantinos Daskalakis; Avinatan Hassidim; Sebastien Roch

doi:10.1016/j.spa.2012.08.004

Global alignment of molecular sequences via ancestral state reconstruction

Alexandr Andoni
, Constantinos Daskalakis
, Avinatan Hassidim
, Sebastien Roch

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

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.

Original language	English
Pages (from-to)	3852-3874
Number of pages	23
Journal	Stochastic Processes and their Applications
Volume	122
Issue number	12
DOIs	https://doi.org/10.1016/j.spa.2012.08.004
State	Published - Dec 2012

Bibliographical note

Funding Information:
The second author was supported by a Sloan Foundation Fellowship and NSF CAREER Award CCF-0953960 . The fourth author was supported by NSF grant DMS-1007144 .

Funding

The second author was supported by a Sloan Foundation Fellowship and NSF CAREER Award CCF-0953960 . The fourth author was supported by NSF grant DMS-1007144 .

Funders	Funder number
National Science Foundation	1248176, CCF-0953960, DMS-1007144
Alfred P. Sloan Foundation

Keywords

Branching processes
Markov models on trees
Phylogenetic inference

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10.1016/j.spa.2012.08.004

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title = "Global alignment of molecular sequences via ancestral state reconstruction",

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.",

keywords = "Branching processes, Markov models on trees, Phylogenetic inference",

author = "Alexandr Andoni and Constantinos Daskalakis and Avinatan Hassidim and Sebastien Roch",

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AU - Andoni, Alexandr

AU - Daskalakis, Constantinos

AU - Hassidim, Avinatan

AU - Roch, Sebastien

N1 - Funding Information: The second author was supported by a Sloan Foundation Fellowship and NSF CAREER Award CCF-0953960 . The fourth author was supported by NSF grant DMS-1007144 .

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Y1 - 2012/12

N2 - 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.

AB - 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.

KW - Branching processes

KW - Markov models on trees

KW - Phylogenetic inference

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JO - Stochastic Processes and their Applications

JF - Stochastic Processes and their Applications

IS - 12

ER -

Global alignment of molecular sequences via ancestral state reconstruction

Abstract

Bibliographical note

Funding

Keywords

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