Large Scale Parallel Inference of Protein and Protein Domain families
type: Dataset
description: Protein domains are recurring independent segment of proteins. The combinatorial arrangement of domains is at the root of the functional and structural diversity of proteins. Several methods have been developed to infer protein domain decomposition and domain family clustering from sequence information alone. MkDom2 is one of those methods. Mkdom2 infers domain families in a greedy fashion. Families are inferred one after the other in order to create a delineation of domains on proteins and a clustering of those domains in families. MkDom2 is instrumental in the building of the ProDom database. The exponential growth of the number of sequences to process as rendered MkDom2 obsolete, it would now take several years to compute a newrelease of ProDom. We present a nous algorithm, MPI_MkDom2, allowing computation of several families at once across a distributed computing platform. MPI_MkDom2 is an asynchronous distributed algorithm managing load balancing to ensure efficient platform usage; it ensures the creation of a non-overlapping partitioning of the whole protein set. A new proximity measure is defined to assess the effect of the parallel computation on the result. We also Propose a second algorithm, MPI_mkDom3, allowing the simultaneous computation of a clustering of protein domains as well as full protein sharing the same domain decomposition.
landing page: https://theses.hal.science/tel-00682495
identifier: NNT: 2011ENSL0643
keyword: bioinformatics
keyword: bioinformatique
keyword: calcul-distribue
keyword: clustering
keyword: distributed-computing
keyword: domain
keyword: domaine
keyword: infoeu-reposemanticsdoctoralthesis
keyword: infoinfo-ohcomputer-science-csother-csoh
keyword: mpi
keyword: protein
keyword: proteine
keyword: theses
issued: 2026-05-23T12:47:46.242513
modified: 2026-05-23T12:47:46.242519
language: en
contact point: Organization
  fn: CCSD

test_moissonnage_selune
type: Agent

Large Scale Parallel Inference of Protein and Protein Domain families
type: Distribution
format: HTML
access URL: https://theses.hal.science/tel-00682495
issued: 2026-05-23T12:47:46.300628
modified: 2026-05-23T12:47:46.206958