{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T07:19:32Z","timestamp":1774768772564,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: With hundreds of completely sequenced microbial genomes available, and advancements in DNA microarray technology, the detection of genes in microbial communities consisting of hundreds of thousands of sequences may be possible. The existing strategies developed for DNA probe design, geared toward identifying specific sequences, are not suitable due to the lack of coverage, flexibility and efficiency necessary for applications in metagenomics.<\/jats:p><jats:p>Methods: ProDesign is a tool developed for the selection of oligonucleotide probes to detect members of gene families present in environmental samples. Gene family-specific probe sequences are generated based on specific and shared words, which are found with the spaced seed hashing algorithm. To detect more sequences, those sharing some common words are re-clustered into new families, then probes specific for the new families are generated.<\/jats:p><jats:p>Results: The program is very flexible in that it can be used for designing probes for detecting many genes families simultaneously and specifically in one or more genomes. Neither the length nor the melting temperature of the probes needs to be predefined. We have found that ProDesign provides more flexibility, coverage and speed than other software programs used in the selection of probes for genomic and gene family arrays.<\/jats:p><jats:p>Availability: ProDesign is licensed free of charge to academic users. ProDesign and Supplementary Material can be obtained by contacting the authors. A web server for ProDesign is available at http:\/\/www.uhnresearch.ca\/labs\/tillier\/ProDesign\/ProDesign.html<\/jats:p><jats:p>Contact: \u00a0e.tillier@utoronto.ca or fsz@ncic.ac.cn<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm114","type":"journal-article","created":{"date-parts":[[2007,3,29]],"date-time":"2007-03-29T00:32:41Z","timestamp":1175128361000},"page":"1195-1202","source":"Crossref","is-referenced-by-count":32,"title":["A fast and flexible approach to oligonucleotide probe design for genomes and gene families"],"prefix":"10.1093","volume":"23","author":[{"given":"Shengzhong","family":"Feng","sequence":"first","affiliation":[{"name":"1 Institute of Computing Technology, Chinese Academy of Sciences, China, 2Ontario Cancer Institute, University Health Network, Toronto, Canada and 3Department of Medical Biophysics, University of Toronto, Canada"},{"name":"1 Institute of Computing Technology, Chinese Academy of Sciences, China, 2Ontario Cancer Institute, University Health Network, Toronto, Canada and 3Department of Medical Biophysics, University of Toronto, Canada"}]},{"given":"Elisabeth R.M.","family":"Tillier","sequence":"additional","affiliation":[{"name":"1 Institute of Computing Technology, Chinese Academy of Sciences, China, 2Ontario Cancer Institute, University Health Network, Toronto, Canada and 3Department of Medical Biophysics, University of Toronto, Canada"},{"name":"1 Institute of Computing Technology, Chinese Academy of Sciences, China, 2Ontario Cancer Institute, University Health Network, Toronto, Canada and 3Department of Medical Biophysics, University of Toronto, Canada"}]}],"member":"286","published-online":{"date-parts":[[2007,3,28]]},"reference":[{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1093\/nar\/gkf450","article-title":"PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database","volume":"30","author":"Ashelford","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/S0723-2020(00)80031-4","article-title":"A nested array of rRNA targeted probes for the detection and identification of Enterococci by reverse hybridization","volume":"23","author":"Behr","year":"2000","journal-title":"Syst. Appl. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"14332","DOI":"10.1073\/pnas.0504068102","article-title":"Highways of gene sharing in prokaryotes","volume":"102","author":"Beiko","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1046\/j.1462-2920.2003.00450.x","article-title":"Development and validation of a diagnostic microbial microarray for methanotrophs","volume":"5","author":"Bodrossy","year":"2003","journal-title":"Environ. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1142\/S0219720004000983","article-title":"A tutorial of recent developments in the seeding of local alignment","volume":"2","author":"Brown","year":"2004","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1080\/10408410590921736","article-title":"Challenges and opportunities for pathogen detection using DNA Microarrays","volume":"31","author":"Call","year":"2005","journal-title":"Critical Reviews in Microbiology"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3677","DOI":"10.1128\/AEM.67.8.3677-3682.2001","article-title":"Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays","volume":"67","author":"Cho","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"2893","DOI":"10.1093\/bioinformatics\/bth347","article-title":"Picky: oligo microarray design for large genomes","volume":"20","author":"Chou","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"4092","DOI":"10.1093\/bioinformatics\/bti673","article-title":"Design of long oligonucleotide probes for functional gene detection in a microbial community","volume":"21","author":"Chung","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3746","DOI":"10.1093\/nar\/gkg569","article-title":"PROBEmer: a web-based software tool for selecting optimal DNA oligos","volume":"31","author":"Emrich","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"TribeMCL: An eficient algorithm for large-scale detection of protein families","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1101\/gr.130000","article-title":"Horizontal gene transfer in bacterial and archaeal complete genomes","volume":"10","author":"Garcia-Vallv\u00e9","year":"2000","journal-title":"Genome Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"e1331","DOI":"10.1093\/nar\/gnh127","article-title":"Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays","volume":"32","author":"Gordon","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"2397","DOI":"10.1128\/aem.63.6.2397-2402.1997","article-title":"Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology","volume":"63","author":"Guschin","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology","author":"Gusfield","year":"1997"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1128\/AEM.71.7.3753-3760.2005","article-title":"Empirical establishment of oligonucleotide probe design criteria","volume":"71","author":"He","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1111\/j.1365-294X.1995.tb00263.x","article-title":"DNA-based monitoring of total bacterial community structure in environmental samples","volume":"4","author":"Holben","year":"1995","journal-title":"Mol. 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Biol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1093\/bioinformatics\/btg401","article-title":"ROSO: optimizing oligonucleotide probes for microarrays","volume":"20","author":"Reymond","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"4303","DOI":"10.1128\/AEM.70.7.4303-4317.2004","article-title":"Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays","volume":"70","author":"Rhee","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1093\/bioinformatics\/bti112","article-title":"GoArrays: highly dynamic and efficient microarray probe design","volume":"21","author":"Rimour","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1093\/bioinformatics\/18.3.486","article-title":"OligoArray: genome-scale oligonucleotide design for microarrays","volume":"18","author":"Rouillard","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1093\/nar\/gkg426","article-title":"OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach","volume":"31","author":"Rouillard","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1128\/AEM.70.3.1455-1465.2004","article-title":"Development and testing of a DNA microarray to assess nitrogenase (nifH) gene diversity","volume":"70","author":"Steward","year":"2004","journal-title":"Appl. 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Microbiol."},{"key":"2023041104481183900_","first-page":"65","article-title":"Fast and accurate probe selection algorithm for large genomes","volume-title":"IEEE Computer Society Bioinformatics Conference (CSB) In Proceedings of the CSB2003 IEEE Computer Society","author":"Sung","year":"2003"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"664","DOI":"10.2144\/04364RR02","article-title":"Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples","volume":"36","author":"Tiquia","year":"2004","journal-title":"Biotechniques"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/S1369-5274(02)00324-7","article-title":"Microbial diversity and function in soil: from genes to ecosystem","volume":"5","author":"Torsvik","year":"2002","journal-title":"Curr. Opin. Microbiol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/nature02340","article-title":"Community structure and metabolism through reconstruction of microbial genomes from the environment","volume":"28","author":"Tyson","year":"2004","journal-title":"Nature"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1126\/science.1093857","article-title":"Environmental genome shotgun sequencing of the Sargasso Sea","volume":"304","author":"Venter","year":"2004","journal-title":"Science"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1093\/bioinformatics\/btg086","article-title":"Selecting of oligonucleotide probes for protein coding sequences","volume":"19","author":"Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1089\/cmb.2006.13.1355","article-title":"Optimizing multiple spaced seeds for homology search","volume":"13","author":"Xu","year":"2006","journal-title":"J. Comput. Biol."},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1093\/bioinformatics\/18.2.244","article-title":"Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset","volume":"18","author":"Zhang","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1093\/bioinformatics\/bth210","article-title":"Efficient selection of unique and popular oligos for large EST databases","volume":"20","author":"Zheng","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104481183900_","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/S1369-5274(03)00052-3","article-title":"Microarrays for bacterial detection and microbial community analysis","volume":"6","author":"Zhou","year":"2003","journal-title":"Curr. Opin. 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