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This paper presents a query-by-singing/humming method that enables fast melody comparison. The basic idea is to measure the distances between note sequences in the frequency domain instead of time domain. Thanks to the merit of fast Fourier transform, we can convert different-length note sequences into equal-dimension vectors via zero padding. The equal dimensionality allows us to compare the vectors using Euclidean distance directly, which avoids performing time-consuming alignment between sequences. To take both efficiency and effectiveness into account, the proposed fast melody comparison method is combined with dynamic time warping technique into a two-stage sequence matching system. Our experiments conducted using the MIREX 2006 database demonstrate the feasibility of the proposed system.