再测序DNA微阵列的等长变覆盖探针设计方法  

Equal-length-variable-overlay probe design methods of resequencing DNA microarray

作　　者：谢建明[1] 方辉[1] 胡弘[1] 陆祖宏[1] 孙啸[1] 

机构地区：[1]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

出　　处：《东南大学学报（自然科学版）》2004年第2期215-218,共4页Journal of Southeast University：Natural Science Edition

基　　金：国家自然科学基金资助项目 ( 699710 10 );江苏省自然科学基金资助项目 (BK2 0 0 2 0 5 7)

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 .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 variable-length-variable-overlay methods.

关 键 词：探针设计 再测序DNA微阵列 等长变覆盖法 遗传算法 

分 类 号：TP391.7[自动化与计算机技术—计算机应用技术]