Transterm: a database of messenger RNA components and signals

Transterm facilitates studies of messenger RNAs and translational control signals. Each messenger RNA (mRNA) from GenBank is extracted and broken into its functional components, its coding sequence, initiation context, termination context, flanking sequence representing its 5′ UTR (untranslated region), 3′ UTR and translational signals. In addition, numerical parameters characterising each coding region in Transterm, including codon and GC bias, are available. For each species in Transterm, the initiation and termination regions are aligned by their start or stop codons and presented as base frequency matrices and tables of the information content of the bases in the alignments. Users can obtain summaries of characteristics of the mRNAs for species of their choice and search for translational signals both in the Transterm database and in their own sequence. The current release contains data from over 10 000 species, including the complete genomes of 20 prokaryotes and three eukaryotes. Both flat-file and relational database forms of Transterm are accessible via the WWW at http://biochem.otago. ac.nz/Transterm/

Transterm可助力信使RNA（messenger RNA，mRNA）及翻译调控信号的相关研究。该数据库从GenBank中提取每条信使RNA，并将其拆解为各类功能组分，包括编码序列、翻译起始上下文、翻译终止上下文、对应5′非翻译区（untranslated region，UTR）与3′非翻译区的侧翼序列，以及各类翻译信号。此外，Transterm还提供表征各编码区域的多项数值参数，涵盖密码子偏好性与GC碱基偏好性等。针对数据库收录的每一物种，其翻译起始区域与终止区域将分别以起始密码子与终止密码子为基准进行序列比对，并以碱基频率矩阵及比对位点碱基信息含量表格的形式呈现。用户可按需获取选定物种的信使RNA特征汇总信息，同时可在Transterm数据库内或自主上传的序列中检索翻译调控信号。当前版本的Transterm收录了超过10000个物种的相关数据，其中包含20种原核生物与3种真核生物的完整基因组序列。用户可通过万维网访问Transterm的纯文本文件与关系数据库两种形式的资源，访问地址为http://biochem.otago.ac.nz/Transterm/