Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences

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2000
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Abstract
To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals.We have developed a method, that we call 'sister-scanning', for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. A Monte Carlo randomization is done for all columns (positions) within a window and Z-scores are obtained for four real sequences or three real sequences with an outlier that is also randomized. The usefulness of the approach is demonstrated using tobamovirus and luteovirus sequences. Contradictory phylogenetic signals were distinguished in both datasets, as were regions of sequence that contained no clear signal or potentially misleading signals related to compositional similarities. In the tobamovirus dataset, contradictory phylogenetic signals were separated by coding sequences up to a kilobase long that contained no clear signal. Our re-analysis of this dataset using sister-scanning also yielded the first evidence known to us of an inter-species recombination site within a viral RNA-dependent RNA polymerase gene together with evidence of an unusual pattern of conservation in the three codon positions.
Reference Key
openalex_W2143119188 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Mark J. Gibbs, J. Scott Armstrong, Adrian J. Gibbs
Journal BMC Bioinformatics
Year 2000
DOI
10.1093/bioinformatics/16.7.573
URL
https://doi.org/10.1093/bioinformatics/16.7.573
Keywords Keywords not found

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