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Bioinformatics Advance Access published online on September 13, 2005
Bioinformatics, 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@oxfordjournals.org
Received March 4, 2005
Revised July 28, 2005
Accepted September 8, 2005

Article

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

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

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

* To whom correspondence should be addressed.
Yong-Ha Park, E-mail: yhpark{at}kribb.re.kr


  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 data sets 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/.

# These authors contributed equally.
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