CAJ | 학술논문

随着16 SrRNA序列资源的不断丰富,以及寡核苷酸微阵列基因芯片技术的不断进步,检测复杂微生物菌落中的微生物种群构成成为可能.现有的序列特异性探针设计算法缺乏足够的覆盖度、灵活性以及效率,不能满足大规模细菌检测基因芯片的设计要求.很多组特异性探针设计算法的思路多局限于针对某个目标序列组设计唯一的组特异性探针.在很多应用场合,设计单个探针检测组内所有目标序列的目标是很难达到的.因此,设计多个探针通过组合方式进行检测是很有必要的.每个探针能特异性地检测组内一部分目标序列,通过组合就能提高覆盖率.然而,在所有可能的探针组合中找到一个优化的探针组合是很耗时的.提出了一个可行的基于相对熵和遗传算法的组合探针设计算法.
수착16 SrRNA서렬자원적불단봉부,이급과핵감산미진렬기인심편기술적불단진보,검측복잡미생물균락중적미생물충군구성성위가능.현유적서렬특이성탐침설계산법결핍족구적복개도、령활성이급효솔,불능만족대규모세균검측기인심편적설계요구.흔다조특이성탐침설계산법적사로다국한우침대모개목표서렬조설계유일적조특이성탐침.재흔다응용장합,설계단개탐침검측조내소유목표서렬적목표시흔난체도적.인차,설계다개탐침통과조합방식진행검측시흔유필요적.매개탐침능특이성지검측조내일부분목표서렬,통과조합취능제고복개솔.연이,재소유가능적탐침조합중조도일개우화적탐침조합시흔모시적.제출료일개가행적기우상대적화유전산법적조합탐침설계산법.
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.