{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T23:43:18Z","timestamp":1780098198834,"version":"3.54.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"17","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Target-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis.<\/jats:p>\n               <jats:p>Results: In this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment and performed using the Affymetrix platform, contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second type includes oligonucleotides that have a specific target on the genomic DNA and their signals are derived from specific and cross-hybridization components combined together in a total signal. A comparative analysis of hybridization specificity of oligo-probes, as well as their nucleotide sequences and thermodynamic features was performed on the database. The comparison has revealed that hybridization specificity was negatively affected by low stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, including GGG motifs, low sequence complexity and nucleotide composition symmetry.<\/jats:p>\n               <jats:p>Conclusion: Filtering out the probes with defined \u2018negative\u2019 characteristics significantly increases specific hybridization and dramatically decreasing genome-wide cross-hybridization. Selected oligo-probes have two times higher hybridization specificity on average, compared to the probes that were filtered from the analysis by applying suggested cutoff thresholds to the described parameters. A new approach for efficient oligo-probe design is described in our study.<\/jats:p>\n               <jats:p>Contact: \u00a0shabalin@ncbi.nlm.nih.gov or olga.matveeva@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw451","type":"journal-article","created":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T07:53:39Z","timestamp":1472716419000},"page":"i552-i558","source":"Crossref","is-referenced-by-count":14,"title":["Optimization of signal-to-noise ratio for efficient microarray probe design"],"prefix":"10.1093","volume":"32","author":[{"given":"Olga V.","family":"Matveeva","sequence":"first","affiliation":[{"name":"1 Biopolymer Design LLC, Acton, MA 01721, USA"},{"name":"2 Engelhardt Institute of Molecular Biology, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yury D.","family":"Nechipurenko","sequence":"additional","affiliation":[{"name":"2 Engelhardt Institute of Molecular Biology, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgeniy","family":"Riabenko","sequence":"additional","affiliation":[{"name":"3 Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chikako","family":"Ragan","sequence":"additional","affiliation":[{"name":"4 Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nafisa N.","family":"Nazipova","sequence":"additional","affiliation":[{"name":"5 Institute of Mathematical Problems of Biology, Pushchino, Moscow Region, 142290, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksey Y.","family":"Ogurtsov","sequence":"additional","affiliation":[{"name":"6 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Svetlana A.","family":"Shabalina","sequence":"additional","affiliation":[{"name":"6 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,8,29]]},"reference":[{"key":"2023020113273329700_btw451-B1","doi-asserted-by":"crossref","first-page":"9287","DOI":"10.1021\/la051231s","article-title":"Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays","volume":"21","author":"Binder","year":"2005","journal-title":"Langmuir"},{"key":"2023020113273329700_btw451-B2","doi-asserted-by":"crossref","first-page":"e7862","DOI":"10.1371\/journal.pone.0007862","article-title":"Mismatch and G-stack modulated probe signals on SNP microarrays","volume":"4","author":"Binder","year":"2009","journal-title":"PLoS ONE"},{"key":"2023020113273329700_btw451-B3","first-page":"RESEARCH0005","article-title":"Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays","volume":"3","author":"Chudin","year":"2002","journal-title":"Genome Biol"},{"key":"2023020113273329700_btw451-B4","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2105-11-207","article-title":"G-stack modulated probe intensities on expression arrays \u2013 sequence corrections and signal calibration","volume":"11","author":"Fasold","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020113273329700_btw451-B5","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1093\/bioinformatics\/btn570","article-title":"Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays","volume":"25","author":"Furusawa","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020113273329700_btw451-B6","doi-asserted-by":"crossref","first-page":"e53","DOI":"10.1093\/nar\/gkp109","article-title":"The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters","volume":"37","author":"Hooyberghs","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020113273329700_btw451-B7","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1093\/hmg\/11.6.669","article-title":"Classification of common conserved sequences in mammalian intergenic regions","volume":"11","author":"Kondrashov","year":"2002","journal-title":"Hum. 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