{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:14Z","timestamp":1740185114550,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,10,14]],"date-time":"2019-10-14T00:00:00Z","timestamp":1571011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 CA154966"],"award-info":[{"award-number":["U01 CA154966"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005189","name":"Leukemia and Lymphoma Society","doi-asserted-by":"publisher","award":["R0818-14"],"award-info":[{"award-number":["R0818-14"]}],"id":[{"id":"10.13039\/100005189","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017834","name":"UConn Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017834","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Health Center Research Advisory Council Exploratory","award":["401703"],"award-info":[{"award-number":["401703"]}]},{"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":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Current web-based sequence logo analyses for studying domain\u2013peptide interactions are often conducted only on high affinity binders due to conservative data thresholding. We have developed Dynalogo, a combination of threshold varying tool and sequence logo generator written in the R statistical programming language, which allows on-the-fly visualization of binding specificity over a wide range of affinity interactions. Hence researchers can easily explore their dataset without the constraint of an arbitrary threshold. After importing quantitative data files, there are various data filtering and visualizing features available. Using a threshold control, users can easily track the dynamic change of enrichment and depletion of amino acid characters in the sequence logo panel. The built-in export function allows downloading filtered data and graphical outputs for further analyses. Dynalogo is optimized for analysis of modular domain\u2013peptide binding experiments but the platform offers a broader application including quantitative proteomics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Dynalogo application, user manual and sample data files are available at https:\/\/dynalogo.cam.uchc.edu. The source code is available at https:\/\/github.com\/lafontaine-uchc\/dynalogo.<\/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\/btz766","type":"journal-article","created":{"date-parts":[[2019,10,11]],"date-time":"2019-10-11T03:52:25Z","timestamp":1570765945000},"page":"1632-1633","source":"Crossref","is-referenced-by-count":0,"title":["Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data"],"prefix":"10.1093","volume":"36","author":[{"given":"Adam T","family":"Lafontaine","sequence":"first","affiliation":[{"name":"Richard D. Berlin Center for Cell Analysis and Modeling"},{"name":"Department of Genetics and Genome Sciences, University of Connecticut School of Medicine , Farmington, CT 06030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce J","family":"Mayer","sequence":"additional","affiliation":[{"name":"Richard D. Berlin Center for Cell Analysis and Modeling"},{"name":"Department of Genetics and Genome Sciences, University of Connecticut School of Medicine , Farmington, CT 06030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuya","family":"Machida","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genome Sciences, University of Connecticut School of Medicine , Farmington, CT 06030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,14]]},"reference":[{"key":"2023060910375661900_btz766-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":"2023060910375661900_btz766-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-018-2489-3","article-title":"A new sequence logo plot to highlight enrichment and depletion","volume":"19","author":"Dey","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023060910375661900_btz766-B3","doi-asserted-by":"crossref","first-page":"1846","DOI":"10.1074\/mcp.M115.047951","article-title":"A comprehensive immunoreceptor phosphotyrosine-based signaling network revealed by reciprocal protein\u2013peptide array screening","volume":"14","author":"Liu","year":"2015","journal-title":"Mol. 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Biol"},{"key":"2023060910375661900_btz766-B6","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":"2023060910375661900_btz766-B7","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1074\/mcp.M110.001586","article-title":"SH2 domains recognize contextual peptide sequence information to determine selectivity","volume":"9","author":"Shah","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2023060910375661900_btz766-B8","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":"2023060910375661900_btz766-B9","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.celrep.2013.03.001","article-title":"The SH2 domain interaction landscape","volume":"3","author":"Tinti","year":"2013","journal-title":"Cell Rep"},{"key":"2023060910375661900_btz766-B10","doi-asserted-by":"crossref","first-page":"3645","DOI":"10.1093\/bioinformatics\/btx469","article-title":"ggseqlogo: a versatile R package for drawing sequence logos","volume":"33","author":"Wagih","year":"2017","journal-title":"Bioinformatics"},{"key":"2023060910375661900_btz766-B11","doi-asserted-by":"crossref","first-page":"W534","DOI":"10.1093\/nar\/gkx323","article-title":"kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences","volume":"45","author":"Wu","year":"2017","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz766\/30491081\/btz766.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/5\/1632\/50552873\/bioinformatics_36_5_1632.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/5\/1632\/50552873\/bioinformatics_36_5_1632.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T10:38:25Z","timestamp":1686307105000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/5\/1632\/5586980"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,10,14]]},"references-count":11,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2020,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz766","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,3]]},"published":{"date-parts":[[2019,10,14]]}}}