In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and split tRNAs. The full unexpurgated analysis of archaeal tRNA genes remains a challenging task in the field of bioinformatics, because of the presence of various types of disrupted tRNA genes in archaea. Here we suggested a computational method that searched for widely separated genes encoding tRNA halves to generate suppressive variants of missing tRNAs. Considering the existence of split tRNA genes widely separated throughout the genome, we developed our tRNA search algorithm to predict such separated tRNA genes by searching both a conserved terminal 5'- and 3'-motif of tRNA in agreement with the split hypothesis on the basis of cloverleaf prediction and precise in silico determination of bulge-helix-bulge secondary structure at the splice sites. By a comprehensive search for missing tRNA genes, we characterized new variants of selenocysteine tRNA that had been found inserted in Methanopyrus kandleri AV19. Analysis of the complete genome sequence of M. kandleri AV19 revealed the multiple mode of transcription of a non-coding RNA decoding UGA to read selenocysteine (Sec) and suggested further study of the disrupted tRNA genes 002E.