[1]马建民,顾万君,周童,等.一种基于密码子使用偏性的检测型基因芯片设计方法[J].东南大学学报(自然科学版),2002,32(4):581-585.[doi:10.3969/j.issn.1001-0505.2002.04.009]
 Ma Jianmin,Gu Wanjun,Zhou Tong,et al.Method for the design of mRNA detecting genechip based on codon usage bias[J].Journal of Southeast University (Natural Science Edition),2002,32(4):581-585.[doi:10.3969/j.issn.1001-0505.2002.04.009]
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一种基于密码子使用偏性的检测型基因芯片设计方法()
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《东南大学学报(自然科学版)》[ISSN:1001-0505/CN:32-1178/N]

卷:
32
期数:
2002年第4期
页码:
581-585
栏目:
生物医学工程
出版日期:
2002-07-20

文章信息/Info

Title:
Method for the design of mRNA detecting genechip based on codon usage bias
作者:
马建民 顾万君 周童 孙啸 陆祖宏
东南大学吴健雄实验室,南京 210096
Author(s):
Ma Jianmin Gu Wanjun Zhou Tong Sun Xiao Lu Zuhang
Chien-shiung Wu Laboratory, Southeast University, Nanjing 210096, China
关键词:
特定蛋白mRNA检测芯片 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
Keywords:
mRNA detecting genechip codon usage bias C-G selective separation G-T base-pairing probe optimization
分类号:
Q755
DOI:
10.3969/j.issn.1001-0505.2002.04.009
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4.25%.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0.20%.通过上述方法,可以显著提高单位芯片面积的信息检测量.
Abstract:
To decrease the number of possible probes 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.

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备注/Memo

备注/Memo:
基金项目: 国家重大基础研究资助项目(G1998051200)、国家自然科学基金资助项目(69525102).
作者简介: 马建民(1971—), 男, 博士生, jmma@seu.edu.cn; 陆祖宏(联系人),男,博士,教授,博士生导师,zhlu@seu.edu.cn.
更新日期/Last Update: 2002-07-20