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Theoretical Computer Science 395 (2008) 193202 www.elsevier.com/locate/tcs

Summary: Theoretical Computer Science 395 (2008) 193202
Multi-break rearrangements and chromosomal evolution
Max A. Alekseyev, Pavel A. Pevzner
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0114, USA
Most genome rearrangements (e.g., reversals and translocations) can be represented as 2-breaks that break a genome at 2 points
and glue the resulting fragments in a new order. Multi-break rearrangements break a genome into multiple fragments and further
glue them together in a new order. While multi-break rearrangements were studied in depth for k = 2 breaks, the k-break distance
problem for arbitrary k remains unsolved. We prove a duality theorem for multi-break distance problem and give a polynomial
algorithm for computing this distance.
c 2008 Elsevier B.V. All rights reserved.
Keywords: Multi-break; Reversal; Translocation; Transposition; Genome rearrangement; Breakpoint graph; Genomic distance
1. Introduction
Rearrangements are genomic "earthquakes" that change the chromosomal architectures. The fundamental question
in molecular evolution is whether there exist "chromosomal faults" (rearrangement hot-spots) where rearrangements
are happening over and over again. The Random Breakage Model (RBM), proposed by Susumu Ohno in 1970,
postulates that rearrangements happen at "random" genomic positions, and thus there are no rearrangement hot-spots
in mammalian genomes. RBM was embraced by biologists (due to its prophetic prediction power) and has become
the de facto theory of chromosome evolution [1,2]. However, Pevzner and Tesler, 2003 [3] recently refuted RBM and


Source: Alekseyev, Max - Department of Computer Science and Engineering, University of South Carolina


Collections: Biotechnology; Computer Technologies and Information Sciences