Exploring Sequence Alignment Algorithms on FPGA-based Heterogeneous Architectures

Xin Chang, Fernando A. Escobar, Carlos Valderrama, Vincent Robert

    Research output: Chapter in book/volumeContribution to conference proceedingsScientificpeer-review

    Abstract

    With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignment algorithms. In addition, we analyze the different types of sequence alignment algorithms and present the taxonomy of FPGA-based sequence alignment implementations. This work will conclude the current solutions and provide a reference to further accelerating sequence alignment on a FPGA-based heterogeneous architecture.
    Original languageUndefined
    Title of host publicationProceedings IWBBIO 2014
    Subtitle of host publicationInternational Work-Conference on Bioinformatics and Biomedical Engineering
    EditorsF. Ortuno, I. Rojas
    Place of PublicationGranada
    Pages330-341
    Number of pages12
    Volume1&2
    Publication statusPublished - 2014

    Keywords

    • Sequence Alignment Algorithm
    • FPGA
    • Heterogeneous Architectures
    • Systolic Array
    • Parallel Computation
    • Hardware Acceleration

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