{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:33:47Z","timestamp":1773282827866,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process.<\/jats:p>\n                  <jats:p>Results: To close this gap we developed, Aptamotif, a computational method for the identification of sequence\u2013structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process.<\/jats:p>\n                  <jats:p>Contact: \u00a0przytyck@ncbi.nlm.nih.gov, Zuben.Sauna@fda.hhs.gov<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts210","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T10:09:18Z","timestamp":1339409358000},"page":"i215-i223","source":"Crossref","is-referenced-by-count":94,"title":["Identification of sequence\u2013structure RNA binding motifs for SELEX-derived aptamers"],"prefix":"10.1093","volume":"28","author":[{"given":"Jan","family":"Hoinka","sequence":"first","affiliation":[{"name":"1 National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA, 2Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia and 3Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA"}]},{"given":"Elena","family":"Zotenko","sequence":"additional","affiliation":[{"name":"1 National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA, 2Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia and 3Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA"}]},{"given":"Adam","family":"Friedman","sequence":"additional","affiliation":[{"name":"1 National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA, 2Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia and 3Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA"}]},{"given":"Zuben E.","family":"Sauna","sequence":"additional","affiliation":[{"name":"1 National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA, 2Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia and 3Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA"}]},{"given":"Teresa M.","family":"Przytycka","sequence":"additional","affiliation":[{"name":"1 National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA, 2Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia and 3Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512351592800_B1","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.jda.2006.03.015","article-title":"Fast detection of common sequence structure patterns in RNAs","volume":"5","author":"Backofen","year":"2007","journal-title":"J. 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