{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T04:52:30Z","timestamp":1771476750451,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"23","funder":[{"name":"Genome Canada to NJP"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,1]]},"abstract":"<jats:p>Summary: Gene Slider helps visualize the conservation and entropy of orthologous DNA and protein sequences by presenting them as one long sequence logo that can be zoomed in and out of, from an overview of the entire sequence down to just a few residues at a time. A search function enables users to find motifs such as cis-elements in promoter regions by simply \u2018drawing\u2019 a sequence logo representation of the desired motif as a query. In addition to displaying user-supplied FASTA files, our demonstration version of Gene Slider loads and displays a rich database of 90\u00a0000+\u2009conserved non-coding regions across the Brassicaceae indexed to the TAIR10 Col-0 Arabidopsis thaliana sequence. It also displays transcription factor binding sites, enabling easy identification of regions that are both conserved across multiple species and may contain transcription factor binding sites.<\/jats:p>\n               <jats:p>Availability and Implementation: Freely available on the web at: http:\/\/www.bar.utoronto.ca\/GeneSlider and also as an app on http:\/\/araport.org. Website implemented in JavaScript and Processing.js with all major browsers supported. Source code available under GNU GPLv2 at SourceForge: https:\/\/sourceforge.net\/projects\/geneslider\/.<\/jats:p>\n               <jats:p>Contact: \u00a0nicholas.provart@utoronto.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw525","type":"journal-article","created":{"date-parts":[[2016,8,14]],"date-time":"2016-08-14T00:17:57Z","timestamp":1471133877000},"page":"3670-3672","source":"Crossref","is-referenced-by-count":10,"title":["Gene Slider: sequence logo interactive data-visualization for education and research"],"prefix":"10.1093","volume":"32","author":[{"given":"Jamie","family":"Waese","sequence":"first","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]},{"given":"Asher","family":"Pasha","sequence":"additional","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]},{"given":"Ting Ting","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]},{"given":"Anna","family":"van Weringh","sequence":"additional","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]},{"given":"David S.","family":"Guttman","sequence":"additional","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]},{"given":"Nicholas J.","family":"Provart","sequence":"additional","affiliation":[{"name":"Department of Cell and Systems Biology\/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada"}]}],"member":"286","published-online":{"date-parts":[[2016,8,13]]},"reference":[{"key":"2023020114073017400_btw525-B1","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023020114073017400_btw525-B2","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020114073017400_btw525-B3","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1038\/ng.2684","article-title":"An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions","volume":"45","author":"Haudry","year":"2013","journal-title":"Nat. Genet"},{"key":"2023020114073017400_btw525-B4","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1109\/TVCG.2011.127","article-title":"Attention and visual memory in visualization and computer graphics","volume":"18","author":"Healey","year":"2012","journal-title":"IEEE Trans. Vis. Comput. Graph"},{"key":"2023020114073017400_btw525-B5","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1093\/pcp\/pcu214","article-title":"A flowering integrator, SOC1, affects stomatal opening in Arabidopsis thaliana","volume":"56","author":"Kimura","year":"2015","journal-title":"Plant Cell Physiol"},{"key":"2023020114073017400_btw525-B6","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkt997","article-title":"JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles","volume":"42","author":"Mathelier","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020114073017400_btw525-B7","doi-asserted-by":"crossref","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","article-title":"Sequence logos: a new way to display consensus sequences","volume":"18","author":"Schneider","year":"1990","journal-title":"Nucleic Acids Res"},{"key":"2023020114073017400_btw525-B8","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1016\/j.celrep.2014.08.019","article-title":"Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana","volume":"8","author":"Sullivan","year":"2014","journal-title":"Cell Rep"},{"key":"2023020114073017400_btw525-B9","doi-asserted-by":"crossref","first-page":"W281","DOI":"10.1093\/nar\/gks469","article-title":"Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion","volume":"40","author":"Thomsen","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020114073017400_btw525-B10","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1111\/j.1365-313X.2005.02437.x","article-title":"The Botany Array Resource: e-Northerns, expression angling, and promoter analyses","volume":"43","author":"Toufighi","year":"2005","journal-title":"Plant J"},{"key":"2023020114073017400_btw525-B11","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.cell.2014.08.009","article-title":"Determination and inference of eukaryotic transcription factor sequence specificity","volume":"158","author":"Weirauch","year":"2014","journal-title":"Cell"},{"key":"2023020114073017400_btw525-B12","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-15-7","article-title":"Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models","volume":"15","author":"Wheeler","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020114073017400_btw525-B13","doi-asserted-by":"crossref","first-page":"25164","DOI":"10.1038\/srep25164","article-title":"Positional distribution of transcription factor binding sites in Arabidopsis thaliana","volume":"6","author":"Yu","year":"2016","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/23\/3670\/49027045\/bioinformatics_32_23_3670.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/23\/3670\/49027045\/bioinformatics_32_23_3670.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:57:40Z","timestamp":1675295860000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/23\/3670\/2525639"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,13]]},"references-count":13,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2016,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw525","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,12,1]]},"published":{"date-parts":[[2016,8,13]]}}}