Split-tRNA-Search

Richard Muench 1 & Lennart Randau 1,2

1 Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, 38106 Braunschweig, GERMANY
2 Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA

Short Introduction

    In some organisms, like the archaeal parasite Nanoarchaeum equitans, tRNA gene sequences can be split and widely separated throughout the genome. The tRNA genes are split into two tRNA-halves after the anticodon-adjacent position 37, the normal location of tRNA introns. Split-tRNA-Search is a program to detect such separated tRNA genes by searching both a conserved terminal 5'- and 3'-motif of tRNA. The information that the 3'-region contains a pairing stretch of 7 nucleotides to a reverse complementary sequence in the 5'-region (the tRNA's acceptor stem) was used to identify matching pairs of tRNA-half genes. In a first step all matching pairs within a distinct distance arising from unsplit tRNAs are removed. The remaining 5' and 3' matches are used to predict possible split tRNAs by similarity of their acceptor stem sequences. In a second step the resulting sequences can be verified using tRNAscan-SE (Lowe & Eddy, 1997).

    Position weight matrices (PWMs) were generated from both a conserved, continuous 3'-region of tRNA genes (nucleotides 54-76) and a 5'-region of tRNA genes (nucleotides 1-16) in an alignment of over 4000 tRNA genes (taken from Marck & Grosjean, 2003).

Download

    The whole package was developed on a Linux platform by use of PHP and the Virtual Footprint (vfp) pattern matching software which was written in C++. PHP 4.3 or higher has to be installed.

References

    PubMed Link
    Marck, C. & Grosjean, H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8, 1189-1232 (2003).

    PubMed Link
    Lowe T. M. & Eddy S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997)

© 2003-2004 by Richard Muench •  Institute of Microbiology • Technical University of Braunschweig •  contact: r.muench@tu-bs.de