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A Pseudo de Bruijn Graph Representation for Discretization Orders for Distance Geometry

Antonio Mucherino 1
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : Instances of the distance geometry can be represented by a simple weighted undirected graph G. Vertex orders on such graphs are discretization orders if they allow for the discretization of the K-dimensional search space of the distance geometry. A pseudo de Bruijn graph B associated to G is proposed in this paper, where vertices correspond to (K+1)-cliques of G, and there is an arc from one vertex to another if, and only if, they admit an overlap, consisting of K vertices of G. This pseudo de Bruijn graph B can be exploited for constructing discretization orders for G for which the consecutivity assumption is satisfied. A new atomic order for protein backbones is presented, which is optimal in terms of length.
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https://hal.inria.fr/hal-01196707
Contributor : Antonio Mucherino <>
Submitted on : Thursday, September 10, 2015 - 11:58:48 AM
Last modification on : Friday, March 6, 2020 - 1:15:24 AM

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  • HAL Id : hal-01196707, version 1

Citation

Antonio Mucherino. A Pseudo de Bruijn Graph Representation for Discretization Orders for Distance Geometry. Proceedings of IWBBIO15, May 2015, Granada, Spain. pp.514-523. ⟨hal-01196707⟩

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