SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level

Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita, Akio Kanai

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


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/.

Original languageEnglish
Pages (from-to)411-418
Number of pages8
JournalIn Silico Biology
Issue number5
Publication statusPublished - 2006 Dec 11


  • Bulge-helix-bulge splicing motif
  • Genome analysis
  • Intron-containing tRNA
  • Software
  • Split tRNA
  • tRNAscan-SE

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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