The Fourier spectrum at a fractional period is often examined when extracting features from biological sequences and time series. It reflects the inner information structure of the sequences. A fractional period is not uncommon in time series. A typical example is the 3.6 period in protein sequences, which determines the $alpha$-helix secondary structure. Computing the spectrum of a fractional period offers a high-resolution insight into a time series. It has thus become an important approach in genomic analysis. However, computing Fourier spectra of fractional periods by the traditional Fourier transform is computationally expensive. In this paper, we present a novel, fast algorithm for directly computing the fractional period spectrum (FPS) of time series. The algorithm is based on the periodic distribution of signal strength at periodic positions of the time series. We provide theoretical analysis, deduction, and special techniques for reducing the computational costs of the algorithm. The analysis of the computational complexity of the algorithm shows that the algorithm is much faster than traditional Fourier transform. Our algorithm can be applied directly in computing fractional periods in time series from a broad of research fields. The computer programs of the FPS algorithm are available at https://github.com/cyinbox/FPS.
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