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

被引：24

作者：

Laslett, D

Canback, B

Andersson, S

机构：

[1] Univ Uppsala, Dept Mol Evolut, SE-75236 Uppsala, Sweden

[2] Murdoch Univ, Perth, WA, Australia

来源：

NUCLEIC ACIDS RESEARCH | 2002年 / 30卷 / 15期

关键词：

D O I：

10.1093/nar/gkf459

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 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.

引用

页码：3449 / 3453

页数：5

共 11 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, SF
Madden, TL
Schaffer, AA
Zhang, JH
Zhang, Z
Miller, W
Lipman, DJ
[J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
[2] Searching for patterns in genomic data
Dsouza, M
Larsen, N
Overbeek, R
[J]. TRENDS IN GENETICS, 1997, 13 (12) : 497 - 498
[3] Emerging views on tmRNA-mediated protein tagging and ribosome rescue
Gillet, R
Felden, B
[J]. MOLECULAR MICROBIOLOGY, 2001, 42 (04) : 879 - 885
[4] tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes:: A two-piece tmRNA functions in Caulobacter
Keiler, KC
Shapiro, L
Williams, KP
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (14) : 7778 - 7783
[5] Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA
Keiler, KC
Waller, PRH
Sauer, RT
[J]. SCIENCE, 1996, 271 (5251) : 990 - 993
[6] tmRDB (tmRNA database)
Knudsen, B
Wower, J
Zwieb, C
Gorodkin, J
[J]. NUCLEIC ACIDS RESEARCH, 2001, 29 (01) : 171 - 172
[7] A bacterial RNA that functions as both a tRNA and an mRNA
Muto, A
Ushida, C
Himeno, H
[J]. TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (01) : 25 - 29
[8] The 10Sa RNA gene of Thermus thermophilus
Op de Bekke, A
Kiefmann, M
Kremerskothen, J
Vornlocher, HP
Sprinzl, M
Brosius, J
[J]. DNA SEQUENCE, 1998, 9 (01): : 31 - 35
[9] C-TERMINAL EXTENSION OF TRUNCATED RECOMBINANT PROTEINS IN ESCHERICHIA-COLI WITH A 10SA RNA DECAPEPTIDE
TU, GF
REID, GE
ZHANG, JG
MORITZ, RL
SIMPSON, RJ
[J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 1995, 270 (16) : 9322 - 9326
[10] TRANSFER-RNA-LIKE STRUCTURES IN 10SA RNAS OF MYCOPLASMA-CAPRICOLUM AND BACILLUS-SUBTILIS
USHIDA, C
HIMENO, H
WATANABE, T
MUTO, A
[J]. NUCLEIC ACIDS RESEARCH, 1994, 22 (16) : 3392 - 3396

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