{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T03:30:43Z","timestamp":1785900643693,"version":"3.56.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Aptamers are synthetic nucleic acid molecules that can bind biological targets in virtue of both their sequence and three-dimensional structure. Aptamers are selected using SELEX, Systematic Evolution of Ligands by EXponential enrichment, a technique that exploits aptamer-target binding affinity. The SELEX procedure, coupled with high-throughput sequencing (HT-SELEX), creates billions of random sequences capable of binding different epitopes on specific targets. Since this technique produces enormous amounts of data, computational analysis represents a critical step to screen and select the most biologically relevant sequences.<\/jats:p>\n               <jats:p>Results: Here, we present APTANI, a computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information. APTANI builds on AptaMotif algorithm, originally implemented to analyze SELEX data; extends the applicability of AptaMotif to HT-SELEX data and introduces new functionalities, as the possibility to identify binding motifs, to cluster aptamer families or to compare output results from different HT-SELEX cycles. Tabular and graphical representations facilitate the downstream biological interpretation of results.<\/jats:p>\n               <jats:p>Availability and implementation: APTANI is available at http:\/\/aptani.unimore.it.<\/jats:p>\n               <jats:p>Contact: \u00a0silvio.bicciato@unimore.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv545","type":"journal-article","created":{"date-parts":[[2015,9,23]],"date-time":"2015-09-23T01:59:09Z","timestamp":1442973549000},"page":"161-164","source":"Crossref","is-referenced-by-count":77,"title":["APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data"],"prefix":"10.1093","volume":"32","author":[{"given":"J.","family":"Caroli","sequence":"first","affiliation":[{"name":"1 Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Taccioli","sequence":"additional","affiliation":[{"name":"1 Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"De La Fuente","sequence":"additional","affiliation":[{"name":"2 Department of Microbiology & Immunology, UM\/Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Serafini","sequence":"additional","affiliation":[{"name":"2 Department of Microbiology & Immunology, UM\/Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Bicciato","sequence":"additional","affiliation":[{"name":"1 Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,9,22]]},"reference":[{"key":"2023020110245400400_btv545-B1","doi-asserted-by":"crossref","first-page":"e230","DOI":"10.1038\/mtna.2015.4","article-title":"FASTAptamer: a bioinformatic toolkit for high-throughput sequence analysis of combinatorial selections","volume":"4","author":"Alam","year":"2015","journal-title":"Mol. Ther. 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