一种基于密码子使用偏性的检测型基因芯片设计方法  

Method for the design of mRNA detecting genechip based on codon usage bias

作　　者：马建民[1] 顾万君[1] 周童[1] 孙啸[1] 陆祖宏[1] 

机构地区：[1]东南大学吴健雄实验室,南京210096

出　　处：《东南大学学报（自然科学版）》2002年第4期581-585,共5页Journal of Southeast University：Natural Science Edition

基　　金：国家重大基础研究资助项目 (G19980 5 12 0 0 );国家自然科学基金资助项目 (695 2 5 10 2 )

摘　　要：首先预测特定蛋白密码子使用概率表 ,以确定序列中各氨基酸的编码密码子 ,这样可以将芯片表面探针的数量减少为原来的 4.47% .然后进一步考虑密码子在编码时的C G选择性分离原则、G T配对原则 ,以进一步将芯片表面探针的数量减少至 4.2 5 % .在对探针特异性要求不高的情况下 ,可以采用最优密码子使用概率表 ,以求最大限度的降低探针的数目 ,这样芯片表面探针的数量可减少到原来的 0 .2 0 % .通过上述方法 。To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.

关 键 词：检测型基因芯片 设计方法 特定蛋白 密码子使用偏性 C-G选择性分离原则 G-T配对原则 探针优化 遗传密码 

分 类 号：Q755[生物学—分子生物学] TN4[电子电信—微电子学与固体电子学]