Parallel H4MSA for Multiple Sequence Alignment

Alvaro Rubio-Largo, Miguel A. Vega-Rodriguez, David L. Gonzalez-Alvarez

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Citations (Scopus)

Abstract

Multiple Sequence Alignment (MSA) is the process of aligning three or more nucleotides/amino-acids sequences at the same time. It is an NP-complete optimization problem where the time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In the multiobjective version of the MSA problem, we simultaneously optimize the alignment accuracy and conservation. In this work, we present a parallel scheme for a multiobjective version of a memetic metaheuristic: Hybrid Multiobjective Memetic Metaheuristics for Multiple Sequence Alignment (H4MSA). In order to evaluate the parallel performance of H4MSA, we use several datasets with different number of sequences (up to 1000 sequences) and compare its parallel performance against other well-known parallel approaches published in the literature, such as MSAProbs, T-Coffee, Clustal O and MAFFT. On the other hand, the results reveals that parallel H4MSA is around 25 times faster than the sequential version with 32 cores.

Original languageEnglish
Title of host publicationProceedings - 13th IEEE International Symposium on Parallel and Distributed Processing with Applications, ISPA 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages242-247
Number of pages6
ISBN (Electronic)9781467379519
ISBN (Print)978-1-4673-7951-9
DOIs
Publication statusPublished - 2 Dec 2015
Event14th IEEE International Conference on Trust, Security and Privacy in Computing and Communications, TrustCom 2015 - Helsinki, Finland
Duration: 20 Aug 201522 Aug 2015

Publication series

NameProceedings - 14th IEEE International Conference on Trust, Security and Privacy in Computing and Communications, TrustCom 2015
Volume3

Conference

Conference14th IEEE International Conference on Trust, Security and Privacy in Computing and Communications, TrustCom 2015
CountryFinland
CityHelsinki
Period20/08/1522/08/15

Keywords

  • Multi-threaded
  • Multiobjective optimization
  • multiple sequence alignment
  • OpenMP

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