ISB Home



- Communication -




Volume 6


Full article

In Silico Biology 6, 0039 (2006); ©2006, Bioinformation Systems e.V.  



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

Junichi Sugahara1,2, Nozomu Yachie1,3, Yasuhiko Sekine4, Akiko Soma4, Motomu Matsui1,2, Masaru Tomita1,2,3 and Akio Kanai1,2,*

1 Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
2 Department of Environmental Information, Keio University, Fujisawa, 252-8520, Japan
3 Bioinformatics Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan
4 Department of Life Science, College of Science, Rikkyo University, 3-34-1, Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan


* Corresponding author
  Email: akio@sfc.keio.ac.jp


Edited by E. Wingender; received May 13, 2006; revised and accepted July 18, 2006; published August 07, 2006

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/.


Keywords: genome analysis, intron-containing tRNA, split tRNA, bulge-helix-bulge splicing motif, software, tRNAscan-SE