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A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency.

Weihua Zheng, Kenli Li, Keqin Li

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |February 19, 2016
    PubMed
    Summary
    This summary is machine-generated.

    Researchers enhanced the Multiple Alignment Fast Fourier Transform (MAFFT) for faster bioinformatics analysis. Novel methods improve correlation computation, significantly boosting the speed of multiple sequence alignment tasks.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Sequence Analysis

    Background:

    • Multiple sequence alignment (MSA) is a fundamental bioinformatics task.
    • Multiple Alignment Fast Fourier Transform (MAFFT) offers speed and accuracy in MSA.
    • Existing MAFFT correlation computation can be further optimized for efficiency.

    Purpose of the Study:

    • To improve the computational efficiency of the MAFFT algorithm.
    • To enhance the speed of multiple sequence alignment through modified correlation computation.

    Main Methods:

    • Utilized novel complex number-based expressions for amino acid and nucleotide sequences.
    • Implemented linear convolution with a limitation for correlation computation.
    • Developed a new Fast Fourier Transform (FFT) algorithm based on conjugate pair split-radix FFT for linear convolution, requiring only real parts of the output.

    Main Results:

    • The modified MAFFT scheme demonstrated a speed increase of 107.58% to 365.74% compared to the original MAFFT for the Falign() function.
    • The new FFT algorithm efficiently computes linear convolution without requiring order permutation.

    Conclusions:

    • The proposed modifications significantly accelerate MAFFT's correlation computation.
    • This enhanced MAFFT offers a faster realization for multiple sequence alignment, benefiting bioinformatics research.