Bioinformatics Vol. 16 no. 7 2000
Pages 573-582
© 2000 Oxford University Press
Original Paper |
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
1 Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia
Received on January 13, 2000
; revised on March 9, 2000
; accepted on March 14, 2000
Motivation: 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.
Results: 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 
-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.
Availability: A program package, SiScan, for use under MS-DOS can be downloaded from http://life.anu.edu.au/with test data and instructions.
Contact: mgibbs{at}rsbs.anu.edu.au; johna{at}rsbs.anu.edu.au; gibbs{at}rsbs.anu.edu.au
* To whom correspondence should be addressed.
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