[1]谢建明,方辉,胡弘,等.再测序DNA微阵列的等长变覆盖探针设计方法[J].东南大学学报(自然科学版),2004,34(2):215-218.[doi:10.3969/j.issn.1001-0505.2004.02.017]
 Xie Jianming,Fang Hui,Hu Hong,et al.Equal-length-variable-overlay probe design methods of resequencing DNA microarray[J].Journal of Southeast University (Natural Science Edition),2004,34(2):215-218.[doi:10.3969/j.issn.1001-0505.2004.02.017]
点击复制

再测序DNA微阵列的等长变覆盖探针设计方法()
分享到:

《东南大学学报(自然科学版)》[ISSN:1001-0505/CN:32-1178/N]

卷:
34
期数:
2004年第2期
页码:
215-218
栏目:
计算机科学与工程
出版日期:
2004-03-20

文章信息/Info

Title:
Equal-length-variable-overlay probe design methods of resequencing DNA microarray
作者:
谢建明 方辉 胡弘 陆祖宏 孙啸
东南大学分子与生物分子电子学教育部重点实验室, 南京 210096
Author(s):
Xie Jianming Fang Hui Hu Hong Lu Zuhong Sun Xiao
Key Laboratory of Molecular and Biomolecular Electronics of Ministry of Education, Southeast University, Nanjing 210096, China
关键词:
探针设计 再测序DNA微阵列 等长变覆盖法 遗传算法
Keywords:
probe design resequencing DNA microarray equal-length-variable-overlay method genetic algorithm
分类号:
TP391.7
DOI:
10.3969/j.issn.1001-0505.2004.02.017
摘要:
针对再测序DNA微阵列的寡核苷酸探针设计,提出了2种等长变覆盖的方法: ① 基于Tm距离的探针优化方法,从冗余探针集中逐步删除具有最大Tm距离的探针; ② 应用遗传算法,将候选探针集编码为染色体,通过选择、交叉和变异等遗传操作得到最大适应度的探针集.这2种方法,都能在探针长度相等的情况下,通过改变相邻探针之间的覆盖度使探针的Tm值尽可能保持一致.实验结果表明:等长变覆盖法得到的探针集整体优于等长移位法和变长变覆盖法的结果,具有更好的杂交条件一致性.
Abstract:
To design the oligonucleotide probes of resequencing DNA microarray, two novel equal-length-variable-overlay approaches have been introduced. One is a probe optimization method based on Tm distance, which deletes gradually the probes with largest Tm distance from the redundant probe library. And the other applies genetic algorithm to the optimization problem of the probes, which can encode the candidate probe sets into chromosomes. After many turns of genetic procedures such as selection, crossover and mutation, the chromosome with greatest fitness will be given which is the solution for this task. Both methods can keep the Tm values of probes with same length similar by changing the overlay scope between the adjacent probes. It shows that equal-length-variable-overlay method can design probes with more similar hybridization features than tiling and varible-length-varible-overlay methods.

参考文献/References:

[1] Lipshutz R,Fodor S,Gingeras T,et al.High density
  synthetic oligonucleotide arrays [J]. Nature Genetics Supplement,1999,21:20-24.
[2] Drmanac R, Crkvenjakov R.Method of sequencing of genomes by hybridization with oligonucleotide probes[P].US Patent,5202231.1993.
[3] Sambrook J,Russell D W,Sambrook J.Molecular cloning:a laboratory manual.3rd ed[M].New York:Cold Spring Harbor Laboratory,2001.1-9.
[4] Hacia J.Resequencing and mutation analysis using oligonucleotides microarrays [J]. Nature Genetics Supplement, 1999,21:42-47.
[5] 孙啸,王晔,赵雨杰,等.一种高密度基因芯片设计的新方法[J].电子学报,2001,29(3):293-296.
  Sun Xiao,Wang Ye,Zhao Yujie,et al.A new method of high density gene chip design [J].Acta Electronica Sinica,2001,19(3):293-296.(in Chinese)
[6] 王晔. 高密度基因芯片的设计、检测模拟及其应用系统实现[D].南京:东南大学生物科学与医学工程系,2000.
[7] Shapiro B A,Wu J C,Bengali D,et al.The massively parallel genetic algorithm for RNA folding:MIMD implementation and population variation[J].Bioinformatics,2001,17(2):137-148.
[8] Hubley R M,Zitzler E,Roach J C.Evolutionary algorithms for the selection of single nucleotide polymorphisms [J].BMC Bioinformatics, 2003,4:30.
[9] Garduno-Juarez R,Morales L B.A genetic algorithm with conformational memories for structure prediction of polypeptides [J].J Biomol Struct Dyn, 2003,21(1):65-88.
[10] 李兴珊,孙啸,袁春伟.基于遗传算法的基因芯片图像网格定位[J].生物物理学报,2002,18(2):223-226.
  Li Xingshan,Sun Xiao,Yuan Chunwei.Automatic gene chip image grid localization using genetic algorithm [J]. ACTA Biophysica Sinica,2002,18(2):223-226.(in Chinese)
[11] Agoston E E,Zbigniew R H.Parameter control in evolutionary algorithms [J].IEEE Trans Evolutionary Computation, 1999,3(2):124-141.

备注/Memo

备注/Memo:
基金项目: 国家自然科学基金资助项目(69971010)、江苏省自然科学基金资助项目(BK2002057).
作者简介: 谢建明(1971—),男,博士生,讲师; 孙啸(联系人),男,博士,教授, 博士生导师,xsun@seu.edu.cn.
更新日期/Last Update: 2004-03-20