title: MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.
abstract: MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively.
  
  
  
  Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at http://msaprobs.sourceforge.net CONTACT: jgonzalezd@udc.esSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Campus de Elviña, Grupo de Arquitectura de Computadores, Universidade da Coruña, 15071 A Coruña, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: González-Domínguez
authors.affiliation: School of Computational Science and Engineering, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Campus de Elviña, Grupo de Arquitectura de Computadores, Universidade da Coruña, 15071 A Coruña, Spain.
authors.forename: Juan
authors.initials: J
authors.lastname: Touriño
authors.affiliation: Institut für Informatik, Johannes Gutenberg Universität Mainz, Staudingerweg 9, Mainz 55128, Germany.
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D011506:Proteins; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins