SARS病毒再测序DNA微阵列的探针设计

Probe Design of Re-sequencing DNA Microarray for SARS Virus

探针设计是SARS病毒再测序DNA微阵列制作的关键步骤 ,为了保证探针的杂交条件尽可能一致 ,采用了作者提出的两种等长变覆盖的探针设计方法 ,即基于Tm距离的算法和遗传算法。针对SARS病毒基因组中的两段特异序列设计了一组探针 ,并与等长移位法和变长变覆盖法的设计结果进行了比较。等长变覆盖法得到的探针集在探针长度一致的情况下 ,探针的Tm值有较小的标准差和变化范围。结果表明 ,等长变覆盖法得到的探针具有更好的杂交条件一致性。

Probe design is the key step of the fabrication of re-sequencing DNA microarray for screening SARS virus.It applied two Equal-Length-Variable-Overlay methods to allow the probes have similar hybridization features,which are Tm-distance-based algorithm and genetic algorithm for probe optimization.The probes for two target sequences from SARS virus genome have been given.Comparing with the results given by tiling method and Variable Length Variable Overlay algorithm,the probes by Equal-Length-Variable-Overlay method can have smaller standard deviation and smaller range of TM while they have the same length.The result showed that Equal-Length-Variable-Overlay method is a promising probe design method which can design probes with similar hybridization features such as Tm and probe length.