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Nucleic Acids Research, 2002, Vol. 30, No. 15 3449-3453
© 2002 Oxford University Press

BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences

Dean Laslett, Bjorn Canback*,1 and Siv Andersson1

Murdoch University, Perth, Western Australia, Australia and 1 Department of Molecular Evolution, University of Uppsala, Norbyvägen 18C, SE-752 36, Uppsala, Sweden

*To whom correspondence should be addressed. Tel: +46 18 471 4203; Fax: +46 18 471 6404; Email: bjorn.canback{at}ebc.uu.se

A computer program, BRUCE, was developed for the identification of transfer-messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNAAla-like secondary structure surrounding a short sequence encoding the tag peptide. In the 57 completely sequenced bacterial genomes where tmRNA genes have been reported previously, BRUCE identified all with no false positives. In addition, BRUCE found 99 of the 100 tmRNAs identified previously in other bacteria, red chloroplasts and cyanelles. The output of the program reports the proposed tRNA secondary structure, the tmRNA gene sequence and the tag peptide.


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