{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T07:19:33Z","timestamp":1774768773220,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0yhpark@kribb.re.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti673","type":"journal-article","created":{"date-parts":[[2005,9,14]],"date-time":"2005-09-14T03:13:12Z","timestamp":1126667592000},"page":"4092-4100","source":"Crossref","is-referenced-by-count":21,"title":["Design of long oligonucleotide probes for functional gene detection in a microbial community"],"prefix":"10.1093","volume":"21","author":[{"given":"Won-Hyong","family":"Chung","sequence":"first","affiliation":[{"name":"Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology 1 \u00a0 1 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"},{"name":"National Genome Information Centre, Korea Research Institute of Bioscience and Biotechnology 4 \u00a0 4 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sung-Keun","family":"Rhee","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Biotechnology Research Institute, Chungbuk National University 2 \u00a0 2 \u00a0 \u00a0 12 Gaeshin-dong, Heungduk-gu, Cheongju, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiu-Feng","family":"Wan","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Miami University 3 \u00a0 3 \u00a0 \u00a0 Oxford, OH 45056, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Woo","family":"Bae","sequence":"additional","affiliation":[{"name":"Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology 1 \u00a0 1 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhe-Xue","family":"Quan","sequence":"additional","affiliation":[{"name":"Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology 1 \u00a0 1 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong-Ha","family":"Park","sequence":"additional","affiliation":[{"name":"Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology 1 \u00a0 1 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"},{"name":"proBionic Corp., Korea Research Institute of Bioscience and Biotechnology 5 \u00a0 5 \u00a0 \u00a0 52, Eun-dong, Yuseong-gu, Daejeon, 305-333, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,9,13]]},"reference":[{"key":"2023061007105448600_b1","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1128\/mr.59.1.143-169.1995","article-title":"Phylogenetic identification and in situ detection of individual microbial cells without cultivation","volume":"59","author":"Amann","year":"1995","journal-title":"Microbiol. 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