Preliminary Analysis of the Cell BE Processor Limitations for Sequence Alignment Applications

  • Sebastian Isaza
  • Friman Sánchez
  • Georgi Gaydadjiev
  • Alex Ramirez
  • Mateo Valero
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5114)


The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multi-core processors. In this paper we present a preliminary study of the Cell BE processor limitations when executing two representative sequence alignment applications (Ssearch and ClustalW). The inherent large parallelism of the targeted algorithms makes them ideal for architectures supporting multiple dimensions of parallelism (TLP and DLP). However, in the case of Cell BE we identified several architectural limitations that need a careful study and quantification.


Local Store Forward Pass Pairwise Sequence Alignment Bioinformatics Application Architectural Limitation 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Sebastian Isaza
    • 1
  • Friman Sánchez
    • 2
  • Georgi Gaydadjiev
    • 1
  • Alex Ramirez
    • 2
    • 3
  • Mateo Valero
    • 2
    • 3
  1. 1.Computer Engineering LabDelft University of TechnologyThe Netherlands
  2. 2.Computer Architecture DepartmentTechnical University of CataloniaSpain
  3. 3.Barcelona Supercomputing Center-CNSSpain

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