{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T14:54:00Z","timestamp":1776869640553,"version":"3.51.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,30]],"date-time":"2020-01-30T00:00:00Z","timestamp":1580342400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institutes of Health Medical Scientist Training Program training grant","award":["5T32GM007288"],"award-info":[{"award-number":["5T32GM007288"]}]},{"DOI":"10.13039\/100000002","name":"NIH","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":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>High-throughput sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment. Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. While several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI-enabled environment. We demonstrate AptCompare\u2019s performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences\u2019 rankings and their binding affinities.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code and pre-built virtual machine images are freely available at https:\/\/bitbucket.org\/shiehk\/aptcompare.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa054","type":"journal-article","created":{"date-parts":[[2020,1,22]],"date-time":"2020-01-22T07:16:51Z","timestamp":1579677411000},"page":"2905-2906","source":"Crossref","is-referenced-by-count":18,"title":["AptCompare: optimized\n                    <i>de novo<\/i>\n                    motif discovery of RNA aptamers via HTS-SELEX"],"prefix":"10.1093","volume":"36","author":[{"given":"Kevin R","family":"Shieh","sequence":"first","affiliation":[{"name":"Department of Medicine , , Brooklyn, NY, USA"},{"name":"Maimonides Medical Center , , Brooklyn, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christina","family":"Kratschmer","sequence":"additional","affiliation":[{"name":"Department of Medicine , , St. Louis, MO, USA"},{"name":"Washington University School of Medicine , , St. Louis, MO, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keith E","family":"Maier","sequence":"additional","affiliation":[{"name":"Vitrisa Therapeutics , Durham, NC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John M","family":"Greally","sequence":"additional","affiliation":[{"name":"Department of Genetics, Albert Einstein College of Medicine , Bronx, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Levy","sequence":"additional","affiliation":[{"name":"Vitrisa Therapeutics , Durham, NC, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron","family":"Golden","sequence":"additional","affiliation":[{"name":"School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway, Galway, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,30]]},"reference":[{"key":"2023013111495768700_btaa054-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. 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