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By adopting the pseudo-random noise (PN) sequences as the guard interval (GI) as well as the training sequence, time domain synchronous orthogonal frequency division multiplexing (TDS-OFDM) outperforms the conventional OFDM using the cyclic prefix (CP) in the spectral efficiency at the cost of the iterative padding subtraction (IPS) in channel estimation (CE). To avoid the high computational complexity of the IPS, an improved frequency domain CE scheme based on a newly designed frame structure is proposed. To further improve the CE accuracy, the time domain training sequences, which are frequency binary (FB) after the fast Fourier transform (FFT), are flexibly padded as the frame header instead of the PN sequences. Theoretical analyses and computer simulations show that the proposed scheme can improve the system performance under the time frequency doubly selective channels, even in the presence of large channel delays in the single frequency networks.