Polynomial-time algorithm for computing translocation distance between genomes
Discrete Applied Mathematics - Special volume on computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
A very elementary presentation of the Hannenhalli-Pevzner theory
Discrete Applied Mathematics
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
Multi-break rearrangements: from circular to linear genomes
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Stability of rearrangement measures in the comparison of genome sequences
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Estimators of translocations and inversions in comparative maps
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
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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 Pevzner-Tesler approach.