BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences
Open Access
- 1 August 2002
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 30 (15) , 3449-3453
- https://doi.org/10.1093/nar/gkf459
Abstract
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.Keywords
This publication has 11 references indexed in Scilit:
- The tmRNA Website: invasion by an intronNucleic Acids Research, 2002
- Emerging views on tmRNA‐mediated protein tagging and ribosome rescueMolecular Microbiology, 2001
- tmRDB (tmRNA database)Nucleic Acids Research, 2001
- tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in CaulobacterProceedings of the National Academy of Sciences, 2000
- A bacterial RNA that functions as both a tRNA and an mRNATrends in Biochemical Sciences, 1998
- The lOSa RNA Gene of Thermus thermophilusDNA Sequence, 1998
- Searching for patterns in genomic dataTrends in Genetics, 1997
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- C-terminal Extension of Truncated Recombinant Proteins in Escherichia coli with a 10Sa RNA DecapeptideJournal of Biological Chemistry, 1995
- tRNA-like structures in 10Sa RNAs ofMycoplasma capricolumandBacillus subtilisNucleic Acids Research, 1994