Brown C M, Stockwell P A, Dalphin M E, Tate W P
Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Nucleic Acids Res. 1994 Sep;22(17):3620-4. doi: 10.1093/nar/22.17.3620.
The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the initiation codon (-20, +10); c) the length, 'G+C%' of the third position of codons (GC3), the 'codon adaptation index' (CAI) and the 'effective number of codons' statistic (Nc); d) summary tables for each organism including total codon usage, stop codon and tetranucleotide stop-signal usage, and matrices tallying base frequencies at each position around the initiation and termination codons. The data are arranged to facilitate investigation of the relationships between the three phases of protein synthesis. The database is available electronically from EMBL.
终止密码子上下文的TransTerm数据库已扩展到包括有义密码子使用情况和起始密码子上下文。该数据库由来自93种生物体的23721个编码序列构建而成。该数据库包含：a）终止密码子周围的序列（-10，+10）；b）起始密码子周围的序列（-20，+10）；c）密码子第三位的长度、“G+C%”（GC3）、“密码子适应指数”（CAI）和“有效密码子数”统计量（Nc）；d）每个生物体的汇总表包括总密码子使用情况、终止密码子和四核苷酸终止信号使用情况，以及起始和终止密码子周围每个位置的碱基频率计数矩阵。数据的排列便于研究蛋白质合成三个阶段之间的关系。该数据库可从EMBL以电子方式获取。
