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