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In this work, the analysis of atrial signals recorded during atrial fibrillation was pursued using two spectral estimators designed for series with missing data: the Lomb periodogram (LP) and the iterative singular spectrum analysis (ISSA). The main aim is to verify if subtraction of the ventricular activity might be avoided by performing spectral analysis on those ECG intervals where such activity is absent, (i.e. the T-Q intervals), at least to estimate the dominant atrial fibrillatory frequency (FF). Recordings coming from the 2004 Computers in Cardiology Termination Challenge Database were analyzed. Fibrillatory frequencies were then compared with those obtained from the analysis of the correspondent atrial signals extracted using a modified average beat subtraction (ABS) technique. We observed that the mean absolute difference was 0.42 plusmn 0.66 Hz for LP, (meanplusmnSD), and 0.39 plusmn 0.64 Hz for ISSA. We concluded that estimation of FF is feasible without applying QRS-T subtraction.