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RECOMB
2004
Springer

Chromosomal breakpoint re-use in the inference of genome sequence rearrangement

9 years 10 months ago
Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
In order to apply gene-order rearrangement algorithms to the comparison of genome sequences, Pevzner and Tesler [9] bypass gene finding and ortholog identification, and use the order of homologous blocks of unannotated sequence as input. The method excludes blocks shorter than a threshold length and ignores small block-internal rearrangements. Here we investigate possible biases introduced by eliminating and amalgamating short blocks, focusing on the notion of "breakpoint re-use" introduced by these authors. Analytic and simulation methods show that re-use is very sensitive to threshold size and to parameters of the rearrangement process. As is pertinent to the comparison of mammalian genomes, large thresholds in the context of high rates of small rearrangements risk randomizing the comparison completely. We suggest a number of mathematical, algorithmic and statistical lines for further developing the PevznerTesler approach. Categories and Subject Descriptors F.2.2 [Analysis...
David Sankoff, Phil Trinh
Added 03 Dec 2009
Updated 03 Dec 2009
Type Conference
Year 2004
Where RECOMB
Authors David Sankoff, Phil Trinh
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