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Bioinformatics Advance Access originally published online on September 13, 2005
Bioinformatics 2005 21(22):4092-4100; doi:10.1093/bioinformatics/bti673
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

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

Won-Hyong Chung 1,4,{dagger}, Sung-Keun Rhee 2,{dagger}, Xiu-Feng Wan 3, Jin-Woo Bae 1, Zhe-Xue Quan 1 and Yong-Ha Park 1,5,*

1Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea
2Department of Microbiology and Biotechnology Research Institute, Chungbuk National University 12 Gaeshin-dong, Heungduk-gu, Cheongju, Korea
3Department of Microbiology, Miami University Oxford, OH 45056, USA
4National Genome Information Centre, Korea Research Institute of Bioscience and Biotechnology 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea
5proBionic Corp., Korea Research Institute of Bioscience and Biotechnology 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea

*To whom correspondence should be addressed.

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.

Availability: http://brcapp.kribb.re.kr/HPD/

Contact: yhpark{at}kribb.re.kr

Supplementary information: http://brcapp.kribb.re.kr/HPD/HPD_Supplementary.doc

Received on March 4, 2005; revised on July 28, 2005; accepted on September 8, 2005

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