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Accelerating Multiple Sequence Alignment with the Cell BE Processor

Accelerating Multiple Sequence Alignment with the Cell BE Processor,10.1093/comjnl/bxp086,The Computer Journal,Hans Vandierendonck,Sean Rul,Koen De Bo

Accelerating Multiple Sequence Alignment with the Cell BE Processor   (Citations: 1)
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Journal: The Computer Journal - CJ , vol. 53, no. 6, pp. 814-826, 2010
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    • ...On the other hand, in [9] ClustalW is parallelized for Cell...
    • ...Vandierendonck et al. [9] have produced a highly optimized version of PA specifically tuned for using 6 SPEs...
    • ...As shown in previous articles [11], [9], [12], GT takes an almost negligible time in most cases, certainly in the ones we are interested in where sequences are in the order of thousand symbols...
    • ...Since PW is mostly compute-bound, performance does not get affected by the job distribution policy. More details can be found in [11], [9]...
    • ...Figure 2b. The FWD and BWD loops are independent (see figure 2a) so we concurrently compute them using two SPEs, as in [9]...
    • ...PW analysis can be found in [11], [9] and GT is not considered as it took less than 1% of the total execution time in all cases analyzed...

    Sebastian Isazaet al. Scalability Analysis of Progressive Alignment on a Multicore

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