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Title 

Design of long oligonucleotide probes for functional gene detection in a microbial community

 

미생물 기능 유전자 분석을 위한 긴 올리고 마이크로어레이 프로브 제작용 소프트웨어 개발

Authors 

Won Hyong ChungS K RheeX F WanJin-Woo BaeZ X QuanYong Ha Park

Publisher 

Oxford University Press (OUP)

Issue Date 

2005

Citation 

Bioinformatics, vol. 21, no. 22, pp. 4092-4100

Keywords 

computer programDNA microarraygene clustergene sequencegenetic algorithmgenetic analysisgenetic variabilitymicrobial geneticsmicroorganismmultigene family

Abstract 

Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. Results: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.

ISSN 

1367-4803

Link 

http://dx.doi.org/10.1093/bioinformatics/bti673

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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