Of mice and men: algorithms for evolutionary distances between genomes with translocation
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genes order and phylogenetic reconstruction: application to γ-proteobacteria
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Power boosts for cluster tests
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
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The increasing number of fully sequenced genomes has led to the study of genome rearrangements. Several approaches have been proposed to solve this problem, all of them being either too complex to be solved efficiently or too simple to be applied to genomes of complex organisms. The latest challenge has been to overcome the problem of having genomes with duplicate genes. This led to the definition of matching models and similarity measures. The idea is to find a matching between genes in two genomes, in order to disambiguate the data of duplicate genes and calculate a similarity measure. The problem becomes that of finding a matching that best preserves the order of genes in two genomes, where gene order is evaluated by a chosen similarity measure. This paper presents a new pseudo-Boolean encoding for computing the exact summed adjacency disruption number for two genomes with duplicate genes. Experimental results on a *** -Proteobacteria data set illustrate the approach.