Bioinformatics Vol. 16 no. 10 2000
Pages 932-940
© 2000 Oxford University Press
Original Paper |
Finding pathogenicity islands and gene transfer events in genome data
1 Department of Zoology, University of
Cambridge, Downing Street, Cambridge CB2 3EH, UK
2 Department of Statistics, Texas A&M
University, USA
Received on January 25, 2000
; revised on April 26, 2000
; accepted on May 15, 2000
Motivation: There is a growing literature on wavelet theory and
wavelet methods showing improvements on more classical techniques,
especially in the contexts of smoothing and extraction of
fundamental components of signals. G+Cpatterns occur at
different lengths (scales) and, for this reason, G+Cplots
are usually difficult to interpret. Current methods for genome
analysis choose a window size and compute a
statistics of the average value for each
window with respect to the whole genome.
Results: Firstly, wavelets are used to smooth
G+Cprofiles to locate characteristic patterns in genome
sequences. The method we use is based on performing a
statistics on the wavelet coefficients of a
profile; thus we do not need to choose a fixed window size, in that
the smoothing occurs at a set of different scales. Secondly, a
wavelet scalogram is used as a measure for sequence profile
comparison; this tool is very general and can be applied to other
sequence profiles commonly used in genome analysis. We show
applications to the analysis of Deinococcus radiodurans
chromosome I, of two strains of Helicobacter pylori (26695,
J99) and two of Neisseria meningitidis (serogroup B strain
MC58 and serogroup A strain Z2491). We report a list of loci that
have different G+Ccontent with respect to the nearby
regions; the analysis of N. meningitidis serogroup B shows
two new large regions with low G+Ccontent that are putative
pathogenicity islands.
Availability: Software and numerical results (profiles, scalograms, high and low frequency components) for all the genome sequences analyzed are available upon request from the authors.
Contact: p.lio{at}zoo.cam.ac.uk
To whom correspondence should be addressed.
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