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

David H.A. Fitch; Morris Goodman

doi:10.1093/bioinformatics/7.2.207

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

David H.A. Fitch, Morris Goodman

Biology and Genomics

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

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 language	English (US)
Pages (from-to)	207-215
Number of pages	9
Journal	Bioinformatics
Volume	7
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/7.2.207
State	Published - Apr 1991

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/7.2.207

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title = "Phylogenetic scanning: A computer-assisted algorithm for mapping gene conversions and other recombinational events",

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.",

author = "Fitch, {David H.A.} and Morris Goodman",

note = "Funding Information: We thank Ben Koop and John Czelusniak for suggestions about the algorithm and Scott Baird for comments on the manuscript. This work was supported by NIH grant HL33940 (to M.G ) and the Center for Molecular Biology at Wayne State University.",

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N2 - 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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Phylogenetic scanning: A computer-assisted algorithm for mapping gene conversions and other recombinational events

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