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Título:
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Exploiting parallelism on progressive alignment methods
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Autor/a:
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Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Notredame, Cedric; Cores Prado, Fernando
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Notas:
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Multiple Sequence Alignment (MSA) constitutes an extremely powerful
tool for important biological applications such as phylogenetic analysis, identification
of conserved motifs and domains and structure prediction. In spite of the improvement
in speed and accuracy introduced by MSA programs, the computational
requirements for large-scale alignments requires high-performance computing and
parallel applications. In this paper we present an improvement to a parallel implementation
of T-Coffee, a widely used MSA package. Our approximation resolves the
bottleneck of the progressive alignment stage on MSA. This is achieved by increasing
the degree of parallelism by balancing the guide tree that drives the progressive
alignment process. The experimental results show improvements in execution time
of over 68% while maintaining the biological accuracy.
This work was supported by the Ministry of Education and Science of Spain under Contract TIN2008-05913 and Consolider CSD2007-00050. |
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Materia(s):
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-T-Coffee
-Multiple Sequence Alignment
-Parallelism |
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Derechos:
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(c) Springer Science+Business Media, LLC, 2011
info:eu-repo/semantics/restrictedAccess |
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Tipo de documento:
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article
publishedVersion |
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Editor:
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Springer Verlag
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Compartir:
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