{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T16:11:57Z","timestamp":1775232717627,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial \u2018black-box\u2019, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality.<\/jats:p><jats:p>Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called \u2018PhylArray\u2019, designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray\/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.<\/jats:p><jats:p>Availability: \u00a0http:\/\/fc.isima.fr\/~rimour\/phylarray\/<\/jats:p><jats:p>Contact: \u00a0pierre.peyret@univ-bpclermont.fr<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm392","type":"journal-article","created":{"date-parts":[[2007,8,14]],"date-time":"2007-08-14T00:12:36Z","timestamp":1187050356000},"page":"2550-2557","source":"Crossref","is-referenced-by-count":37,"title":["PhylArray: phylogenetic probe design algorithm for microarray"],"prefix":"10.1093","volume":"23","author":[{"given":"C\u00e9cile","family":"Militon","sequence":"first","affiliation":[{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische Universit\u00e4t M\u00fcnchen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00e9bastien","family":"Rimour","sequence":"additional","affiliation":[{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische Universit\u00e4t M\u00fcnchen, Germany"},{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische Universit\u00e4t M\u00fcnchen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohieddine","family":"Missaoui","sequence":"additional","affiliation":[{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische Universit\u00e4t M\u00fcnchen, Germany"},{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische Universit\u00e4t M\u00fcnchen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Corinne","family":"Biderre","sequence":"additional","affiliation":[{"name":"1 G\u00e9nomique Int\u00e9gr\u00e9e des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des C\u00e9zeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubi\u00e8re Cedex, France and 3Lehrstuhl f\u00fcr Rechnertechnik und Rechnerorganisation, Institut f\u00fcr Informatik, Technische 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