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

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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
Author(s)
Won Hyong Chung; S K Rhee; X F Wan; Jin-Woo Bae; Z X Quan; Yong Ha Park
Bibliographic Citation
Bioinformatics, vol. 21, no. 22, pp. 4092-4100
Publication Year
2005
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
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/bioinformatics/bti673
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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