Reconstructing a history of recombinations from a set of sequences

John D Kececioglu, Dan Gusfield

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

One of the classic problems in computational biology is the reconstruction of evolutionary history. A recent trend in the area is to increase the explanatory power of the models that are considered by incorporating higher-order evolutionary events that more accurately reflect the mechanisms of mutation at the level of the chromosome. We take a step in this direction by considering the problem of reconstructing an evolutionary history for a set of genetic sequences that have evolved by recombination. Recombination is a non-tree-like event that produces a child sequence by crossing two parent sequences. We present polynomial-time algorithms for reconstructing a parsimonious history of such events for several models of recombination when all sequences, including those of ancestors, are present in the input. We also show that these models appear to be near the limit of what can be solved in polynomial time, in that several natural generalizations are NP-complete.

Original languageEnglish (US)
Pages (from-to)239-260
Number of pages22
JournalDiscrete Applied Mathematics
Volume88
Issue number1-3
StatePublished - Nov 9 1998
Externally publishedYes

Fingerprint

Recombination
Polynomials
Chromosomes
Computational Biology
Polynomial-time Algorithm
Chromosome
Polynomial time
Mutation
NP-complete problem
Model
Higher Order
History

Keywords

  • Bottleneck optimality
  • Computational biology
  • Directed hypergraphs
  • Edit distance
  • Evolutionary trees
  • Recombination

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Applied Mathematics
  • Discrete Mathematics and Combinatorics
  • Theoretical Computer Science

Cite this

Reconstructing a history of recombinations from a set of sequences. / Kececioglu, John D; Gusfield, Dan.

In: Discrete Applied Mathematics, Vol. 88, No. 1-3, 09.11.1998, p. 239-260.

Research output: Contribution to journalArticle

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