There are not enough selenocysteine tRNA sequences to properly evaluate tRNAscan-SE's selenocysteine detection accuracy. Three selenocysteine tRNAs (one each from H. influenzae, M. jannaschii, and C. elegans) were detected in recent genome sequence data. The H. influenzae tRNA, previously unrecognized in the literature, was detected by the prokaryotic selenocysteine-specific routines and covariance model. The tRNA from the distantly related M. jannaschii, however, was detected by the standard EufindtRNA algorithm and general tRNA covariance model. The failure of the specialized routines may have been due in part to the fact that this is the first and only archaebacterial selenocysteine tRNA available to date. For the remaining non-archaeal selenocysteine tRNAs, use of the specialized models boosts covariance model scores from the 20-40 bit range to 45-72 bits. Since accurate tRNA secondary structure prediction relies on correct alignment of the tRNA sequence to the covariance model, use of selenocysteine-specific models for these tRNAs improves the accuracy of structure predictions. A search of the non-redundant database (nrdb) maintained at NCBI revealed no new selenocysteine tRNAs from species for which there was no previously noted sequence.