On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Journal of Computational Biology Year : 2016

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

Abstract

Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches.
Fichier principal
Vignette du fichier
Auth-JCB16.pdf (176.49 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

hal-01388448 , version 1 (24-05-2017)

Identifiers

Cite

Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, et al.. On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. Journal of Computational Biology, 2016, 23 (9), pp.718 - 736. ⟨10.1089/cmb.2015.0220⟩. ⟨hal-01388448⟩

Collections

INRIA INRIA2
131 View
508 Download

Altmetric

Share

Gmail Facebook X LinkedIn More