Phylogenetic scanning

A computer-assisted algorithm for mapping gene conversions and other recombinational events

David Fitch, M. Goodman

Research output: Contribution to journalArticle

Abstract

An algorithm, 'phylogenetic scanning', is described for mapping gene conversion events where comparative DNA sequence data are available from different species. In this algorithm, sets of hypothetical phylogenetic trees are constructed that describe possible sequence relationships due to gene conversions in different species lineages; these trees are then evaluated by the principle of parsimony at intervals in the sequence alignment. When used to map gene conversion events that occurred between the pair of γ-globin genes of higher primates, the algorithm gives results nearly identical to those obtained using a tedious manual approach. Suggestions are also provided for adaptation of this procedure to the analysis of other recombination events.

Original languageEnglish (US)
Pages (from-to)207-215
Number of pages9
JournalComputer Applications in the Biosciences
Volume7
Issue number2
StatePublished - 1991

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Gene Conversion
Phylogenetics
Scanning
Genes
Gene
Globins
Sequence Alignment
DNA sequences
Parsimony
Primates
Genetic Recombination
Phylogenetic Tree
Recombination
DNA Sequence
Interval

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Molecular Biology
  • Statistics and Probability
  • Computational Mathematics
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Biochemistry

Cite this

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abstract = "An algorithm, 'phylogenetic scanning', is described for mapping gene conversion events where comparative DNA sequence data are available from different species. In this algorithm, sets of hypothetical phylogenetic trees are constructed that describe possible sequence relationships due to gene conversions in different species lineages; these trees are then evaluated by the principle of parsimony at intervals in the sequence alignment. When used to map gene conversion events that occurred between the pair of γ-globin genes of higher primates, the algorithm gives results nearly identical to those obtained using a tedious manual approach. Suggestions are also provided for adaptation of this procedure to the analysis of other recombination events.",
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