{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:37:59Z","timestamp":1740184679173,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,9,30]],"date-time":"2016-09-30T00:00:00Z","timestamp":1475193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG006860"],"award-info":[{"award-number":["HG006860"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approaches continues to emerge, a universal framework is needed to quantitatively ensure consistent and high-quality data. We present SEQualyzer, a visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure profiling experiments. Our methods rely on features common to a wide range of protocols and can serve as standards for quality control and analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>SEQualyzer is written in R, is platform-independent, and is freely available at http:\/\/bme.ucdavis.edu\/aviranlab\/SEQualyzer.<\/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\/btw627","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"441-443","source":"Crossref","is-referenced-by-count":8,"title":["SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data"],"prefix":"10.1093","volume":"33","author":[{"given":"Krishna","family":"Choudhary","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luyao","family":"Ruan","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fei","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan","family":"Shih","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sharon","family":"Aviran","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,30]]},"reference":[{"key":"2023020204411634000_btw627-B1","doi-asserted-by":"crossref","first-page":"11069","DOI":"10.1073\/pnas.1106541108","article-title":"Modeling and automation of sequencing-based characterization of RNA structure","volume":"108","author":"Aviran","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020204411634000_btw627-B2","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.1261\/rna.043844.113","article-title":"Rational experiment design for sequencing-based RNA structure mapping","volume":"20","author":"Aviran","year":"2014","journal-title":"RNA"},{"key":"2023020204411634000_btw627-B3","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btw501","article-title":"Metrics for rapid quality control in RNA structure probing experiments","author":"Choudhary","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020204411634000_btw627-B4","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1073\/pnas.0806929106","article-title":"Accurate SHAPE-directed RNA structure determination","volume":"106","author":"Deigan","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. 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