{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:07:54Z","timestamp":1762297674581},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays.<\/jats:p>\n               <jats:p>Results: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contaminated environmental sample proved the specificity and the sensitivity of probes designed with the HiSpOD program.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/fc.isima.fr\/~g2im\/hispod\/.<\/jats:p>\n               <jats:p>Contact: \u00a0pierre.peyret@univ-bpclermont.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq712","type":"journal-article","created":{"date-parts":[[2011,1,8]],"date-time":"2011-01-08T01:26:38Z","timestamp":1294449998000},"page":"641-648","source":"Crossref","is-referenced-by-count":30,"title":["HiSpOD: probe design for functional DNA microarrays"],"prefix":"10.1093","volume":"27","author":[{"given":"Eric","family":"Dugat-Bony","sequence":"first","affiliation":[{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"},{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohieddine","family":"Missaoui","sequence":"additional","affiliation":[{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"},{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Peyretaillade","sequence":"additional","affiliation":[{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"},{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire 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France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Gouinaud","sequence":"additional","affiliation":[{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, F-63000 Clermont-Ferrand, 4UMR CNRS 6158, LIMOS, F-63173 Aubi\u00e8re and 5Clermont Universit\u00e9, Universit\u00e9 d'Auvergne, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, France"},{"name":"1 Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, Laboratoire Microorganismes: G\u00e9nome et Environnement, BP 10448, F63000, Clermont-Ferrand, 2UMR CNRS 6023, Universit\u00e9 Blaise Pascal, 63000 Clermont-Ferrand, 3Clermont Universit\u00e9, Universit\u00e9 Blaise Pascal, LIMOS, BP 10448, 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