ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
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DOI：
10.1093/nar/gkh152
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Canback, B
中科院分区：
文献类型：
--
作者：
Laslett, D;Canback, B
一个名为ARAGORN的计算机程序可以识别tRNA和tmRNA基因。该程序采用启发式算法来预测tRNA二级结构，基于与公认的tRNA共识序列的同源性和形成碱基配对的三叶草的能力。tmRNA基因是使用改良版的BRUCE程序进行鉴定的。ARAGORN对1290个真细菌、真核生物和古细菌tRNA基因的检测灵敏度达到99%，检测tmRNA数据库中所有完整的tmRNA序列，提高了BRUCE程序的性能。最近发现的tmRNA基因在叶绿体的两个物种从“绿色”藻类谱系被检测到。该程序的输出报告了拟议的tRNA二级结构，对于tmRNA基因，报告了tRNA结构域的二级结构，tmRNA基因序列，标签肽和具有匹配tmRNA肽标签的生物体列表。
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 of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.