TY - JOUR
T1 - Sorting genomes with centromeres by translocations
AU - Ozery-Flato, Michal
AU - Shamir, Ron
PY - 2008/9/1
Y1 - 2008/9/1
N2 - A centromere is a special region in the chromosome that plays a vital role during cell division. Every new chromosome created by a genome rearrangement event must have a centromere in order to survive. This constraint has been ignored in the computational modeling and analysis of genome rearrangements to date. Unlike genes, the different centromeres are indistinguishable, they have no orientation, and only their location is known. A prevalent rearrangement event in the evolution of multi-chromosomal species is translocation (i.e., the exchange of tails between two chromosomes). A translocation may create a chromosome with no centromere in it. In this paper, we study for the first time centromeres-aware genome rearrangements. We present a polynomial time algorithm for computing a shortest sequence of translocations transforming one genome into the other, where all of the intermediate chromosomes must contain centromeres. We view this as a first step towards analysis of more general genome rearrangement models that take centromeres into consideration.
AB - A centromere is a special region in the chromosome that plays a vital role during cell division. Every new chromosome created by a genome rearrangement event must have a centromere in order to survive. This constraint has been ignored in the computational modeling and analysis of genome rearrangements to date. Unlike genes, the different centromeres are indistinguishable, they have no orientation, and only their location is known. A prevalent rearrangement event in the evolution of multi-chromosomal species is translocation (i.e., the exchange of tails between two chromosomes). A translocation may create a chromosome with no centromere in it. In this paper, we study for the first time centromeres-aware genome rearrangements. We present a polynomial time algorithm for computing a shortest sequence of translocations transforming one genome into the other, where all of the intermediate chromosomes must contain centromeres. We view this as a first step towards analysis of more general genome rearrangement models that take centromeres into consideration.
KW - Combinatorics
KW - Comparative genomics
KW - Genome rearrangements
KW - Sorting by translocations
UR - http://www.scopus.com/inward/record.url?scp=51349152408&partnerID=8YFLogxK
U2 - 10.1089/cmb.2007.0136
DO - 10.1089/cmb.2007.0136
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C2 - 18652529
AN - SCOPUS:51349152408
SN - 1066-5277
VL - 15
SP - 793
EP - 812
JO - Journal of Computational Biology
JF - Journal of Computational Biology
IS - 7
ER -