Design of 16 S rRNA-based Oligonucleotide Array Using Group-specific Non-unique Probes in Large Scale Bacteria Detection

VernacularTitle:基于组合探针识别的大规模细菌分类16SrRNA基因芯片设计
Author: Yibo WU ; Xiaochen BO ; Lirong YAN ; Guangchuang YU ; Hui LIU ; Hanchang SUN ; Hongwei XIE ; Shengqi WANG
Publication Type:Journal Article
Keywords: 16 S rRNA; oligonucleotide microarray; group-specific probes
From: Progress in Biochemistry and Biophysics 2009;36(8):1025-1034
CountryChina
Language:Chinese
Abstract: With thousands of sequenced 16 S rRNA genes available,and advancements in oligonucleotide microarray technology,the detection of microorganisms in microbial communities consisting of hundreds of species may be possible.The existing algorithms developed for sequence-specific probe design are not suitable for applications in large-scale bacteria detection due to the lack of coverage,flexibility and efficiency.Many other strategies developed for group-specific probe design focus on how to find a unique group-specific probe that can specifically detect all target sequences of a group.Unique group-specific probe for each group can not always be found.Hence,it is necessary to design non-unique probes.Each probe can specifically detect target sequences of a different subgroup.Combination of multiple probes can achieve higher coverage.However,it is a time-consuming task to evaluate all possible combinations.A feasible algorithm using relative entropy and genetic algorithm (GA) to design group-specific non-unique probes was presented.