Method Of Probe Design For Oligonucleotide Array And Construction Of On-line Application System

Microarray technology has attracting wider scientists'attention and applied in various fields of life science research in recent years. Usually the procedure of an array experiment includes probe design, chip manufacturing, sample labeling, hybridization, image acquisition and data analysis. As the primary step, the good quality of the designed probes is a prerequisite for the successful results of an array experiment. According to the requirements on consistency, sensitivity and specificity of the probes, multiply criteria should be established for the screening of the candidate probes to select the qualified probes meeting the above requirements, that's to say that the selected probes should be able to bind their targets specifically but not to un-targets and all the probes in the same array have similar hybridization attributes. As much computation work is involved in the process of the probe design, the skills and methods of bioinformatics can be appropriately applied in accomplishing this task.There are two types of microarray, including oligonucleotide array and cDNA array. As the target type of the arrays'probes could be genomic DNA, gene, transcript or exon, in this study we firstly proposed a target-type specific probe design method with the processes of the probe design for different types of targets being different. Comprehensive criteria were set up for the screening of candidate probes based on the requirements on consistency, sensitivity and specificity. For those candidate probes failing to meet the criteria for qualified probes, a scoring method was established to evaluate the distance between each candidate probe and the criteria. In case of no qualified probes being found for a target, users can still find the optimal probe with this scoring strategy. Finally, an on-line oligonucleotide array probe design system, named omniProbe, was developed. A user can submit a probe design job and a notification will be sent by e-mail when the probe design job has been done. The user can check the result on-line and download all result files directly.In conclusion, the method of the probe design proposed in this dissertation is applicable to different target types of oligonucleotide array, and users can use our on-line application system of this design method, omniProbe, to fulfill their probe design tasks conveniently.