Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
Genomic features in the breakpoint regions between syntenic blocks
1 Hillcrest High School, Ottawa K1G 2L7, Canada, 2 Genetics Department, Trinity College, University of Dublin, Dublin 2, Ireland and 3 Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa K1N 6N5, Canada
Received on January 15, 2004; accepted on March 1, 2004
Motivation: We study the largely unaligned regions between the syntenic blocks conserved in humans and mice, based on data extracted from the UCSC genome browser. These regions contain evolutionary breakpoints caused by inversion, translocation and other processes.
Results: We suggest explanations for the limited amount of genomic alignment in the neighbourhoods of breakpoints. We discount inferences of extensive breakpoint reuse as artefacts introduced during the reconstruction of syntenic blocks. We find that the number, size and distribution of small aligned fragments in the breakpoint regions depend on the origin of the neighbouring blocks and the other blocks on the same chromosome. We account for this and for the generalized loss of alignment in the regions partially by artefacts due to alignment protocols and partially by mutational processes operative only after the rearrangement event. These results are consistent with breakpoints occurring randomly over virtually the entire genome.
Contact: sankoff{at}uottawa.ca
* To whom correspondence should be addressed.
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