Affiliations: Institute for Advanced Biosciences, Keio University,
Tsuruoka, 997-0017, Japan | Department of Environmental Information, Keio
University, Fujisawa, 252-8520, Japan | Bioinformatics Program, Graduate School of Media and
Governance, Keio University, Fujisawa, 252-8520, Japan | Department of Life Science, College of Science, Rikkyo
University, 3-34-1, Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan
Abstract: In the archaea, some tRNA precursors contain intron(s) not only in
the anticodon loop region but also in diverse sites of the gene
(intron-containing tRNA or cis-spliced tRNA). The parasite
Nanoarchaeum equitans, a member of the Nanoarchaeota kingdom, creates
functional tRNA from separate genes, one encoding the 5'-half and the other the
3'-half (split tRNA or trans-spliced tRNA). Although recent genome
projects have revealed a huge amount of nucleotide sequence data in the
archaea, a comprehensive methodology for intron-containing and split tRNA
searching is yet to be established. We therefore developed SPLITS, which is
aimed at searching for any type of tRNA gene and is especially focused on
intron-containing tRNAs or split tRNAs at the genome level. SPLITS initially
predicts the bulge-helix-bulge splicing motif (a well-known, required structure
in archaeal pre-tRNA introns) to determine and remove the intronic regions of
tRNA genes. The intron-removed DNA sequences are automatically queried to
tRNAscan-SE. SPLITS can predict known tRNAs with single introns located at
unconventional sites on the genes (100%, tRNAs with double introns
(85.7%, and known split tRNAs (100%). Our program will be very useful for
identifying novel tRNA genes after completion of genome projects. The SPLITS
source code is freely downloadable at http://splits.iab.keio.ac.jp/.
