RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression
RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression
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DOI：
10.1093/bioinformatics/btq458
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发表时间：
2010-10-01
期刊：
影响因子：
5.8
通讯作者：
Lee, Doheon
中科院分区：
文献类型：
--
作者：
Na, Dokyun;Lee, Doheon
动机：RBSDesigner预测现有mRNA序列的翻译效率，并为给定的编码序列（CDS）设计合成核糖体结合位点（RBS），以产生所需的蛋白质表达水平。该程序实现了Na等人（Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC系统生物学，4，71）。该程序还结合了Shine-Dalgarno（SD）序列和AUG密码子之间的间隔区长度对翻译效率的影响，这对于将fMet-tRNA掺入核糖体至关重要。RBSDesigner提供了一个图形用户界面（GUI），方便设计合成RBS。
Motivation: RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol., 4, 71). The program additionally incorporates the effect on translation efficiency of the spacer length between a Shine-Dalgarno (SD) sequence and an AUG codon, which is crucial for the incorporation of fMet-tRNA into the ribosome. RBSDesigner provides a graphical user interface (GUI) for the convenient design of synthetic RBSs.