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A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity(More)
MOTIVATION Mitochondrial genomes encode their own transfer RNAs (tRNAs). These are often degenerate in sequence and structure compared to tRNAs in their bacterial ancestors. This is one of the reasons why current tRNA gene predictor programs perform poorly identifying mitochondrial tRNA genes. As a consequence there is a need for a new program with the(More)
A computer program, BRUCE, was developed for the identification of transfer-messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNA(Ala)-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(More)
Accurate estimation of biodegradation rates during remediation of petroleum impacted soil and groundwater is critical to avoid excessive costs and to ensure remedial effectiveness. Oxygen depth profiles or oxygen consumption over time are often used separately to estimate the magnitude and timeframe for biodegradation of petroleum hydrocarbons in soil and(More)
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