New PDF release: Algorithms in Bioinformatics: 8th International Workshop,

By Eric Tannier, Chunfang Zheng, David Sankoff (auth.), Keith A. Crandall, Jens Lagergren (eds.)

ISBN-10: 3540873600

ISBN-13: 9783540873600

ISBN-10: 3540873619

ISBN-13: 9783540873617

This e-book constitutes the refereed court cases of the eighth overseas Workshop on Algorithms in Bioinformatics, WABI 2008, held in Karlsruhe, Germany, in September 2008 as a part of the ALGO 2008 meeting.

The 32 revised complete papers offered including the summary of a keynote speak have been conscientiously reviewed and chosen from eighty one submissions. All present problems with algorithms in bioinformatics are addressed, achieving from mathematical instruments to experimental experiences of approximation algorithms and experiences on major computational analyses. the subjects diversity in organic applicability from genome mapping, to series meeting, to microarray caliber, to phylogenetic inference, to molecular modeling.

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Additional info for Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings

Sample text

However, this method is still primitive needs further improvements. In recent years, the double-cut-and-join (DCJ) distance has attracted much attention. We find that the lower bound 24 M. Zhang, W. Arndt, and J. Tang used in this paper is indeed very similar to the DCJ distance [2], thus it may be relatively easy to extend our work and develop a new DCJ median solver. Acknowledgments WA and JT are supported by US National Institutes of Health (NIH grant number R01 GM078991-01). 60473099. References 1.

Gq ) with node set V and edge multiset M(G1 ) ∪M(G2 ), . . , ∪M(Gq ). Note that for two matchings M(Gj ) and M(Gk ), j = k, some edges may be common in both matchings, but they are considered distinct parallel edges in the MB graph G(G1 , G2 , . . , Gq ). In this paper, q always equals three. Let Q := {1, . . , q} and let τ be a genome, γ(τ ) = k∈Q c˜(τ, Gk ). By Equation 1, for any genome σ, δ(σ) = k∈Q dHP (σ, Gk ) ≥ qn − γ(σ), where n is the number of genes. We introduce the Pseudo-Cycle Median Problem (PMP): given undirected genomes G1 , G2 , .

Sankoff -3 (+5) -6 (+7) -3 (+5) -6 (+7) +4 (+6) +1 (-7) +4 (+6) +1 (-7) (a) (b) Fig. 6. The contracted twin graph (a) and contracted symmetric graph (b). The contracted graphs are generated from a twin median graph by contracting 0-edges. Dashed edges are from the complementary subgraphs and the half-solid-half-dashed ones are the connecting edges. ◦• Next we investigate the difference between a twin median graph M and a sym◦◦ metric median graph M , in terms of the number of DCJ operations needed to transform one into another.

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Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings by Eric Tannier, Chunfang Zheng, David Sankoff (auth.), Keith A. Crandall, Jens Lagergren (eds.)


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