The Reconstruction of Doubled Genomes
SIAM Journal on Computing
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
Assignment of Orthologous Genes via Genome Rearrangement
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the tandem duplication-random loss model of genome rearrangement
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Whole Genome Duplications and Contracted Breakpoint Graphs
SIAM Journal on Computing
Analysis of segmental duplications via duplication distance
Bioinformatics
Reconstructing the evolutionary history of complex human gene clusters
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
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Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics consisting of pieces of multiple other segmental duplications. This complex genomic organization complicates analysis of the evolutionary history of these sequences. Earlier, we introduced a genomic distance, called duplication distance, that computes the most parsimonious way to build a target string by repeatedly copying substrings of a source string. We also showed how to use this distance to describe the formation of segmental duplications according to a two-step model that has been proposed to explain human segmental duplications. Here we describe polynomial-time exact algorithms for several extensions of duplication distance including models that allow certain types of substring deletions and inversions. These extensions will permit more biologically realistic analyses of segmental duplications in genomes.