{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T02:04:27Z","timestamp":1760061867973,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,21]],"date-time":"2019-06-21T00:00:00Z","timestamp":1561075200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Statistical dependencies are present in a variety of sequence data, but are not discernible from traditional sequence logos. Here, we present the R package DepLogo for visualizing inter-position dependencies in aligned sequence data as dependency logos. Dependency logos make dependency structures, which correspond to regular co-occurrences of symbols at dependent positions, visually perceptible. To this end, sequences are partitioned based on their symbols at highly dependent positions as measured by mutual information, and each partition obtains its own visual representation. We illustrate the utility of the DepLogo package in several use cases generating dependency logos from DNA, RNA and protein sequences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The DepLogo R package is available from CRAN and its source code is available at https:\/\/github.com\/Jstacs\/DepLogo.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz507","type":"journal-article","created":{"date-parts":[[2019,6,13]],"date-time":"2019-06-13T11:10:56Z","timestamp":1560424256000},"page":"4812-4814","source":"Crossref","is-referenced-by-count":5,"title":["DepLogo: visualizing sequence dependencies in R"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2081-6405","authenticated-orcid":false,"given":"Jan","family":"Grau","sequence":"first","affiliation":[{"name":"Institute of Computer Science, Martin Luther University Halle-Wittenberg , Halle (Saale), Germany"}]},{"given":"Martin","family":"Nettling","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Martin Luther University Halle-Wittenberg , Halle (Saale), Germany"}]},{"given":"Jens","family":"Keilwagen","sequence":"additional","affiliation":[{"name":"Institute for Biosafety in Plant Biotechnology, Julius K\u00fchn-Institut (JKI) , Quedlinburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,6,21]]},"reference":[{"key":"2023013108353643800_btz507-B1","doi-asserted-by":"crossref","first-page":"e85629.","DOI":"10.1371\/journal.pone.0085629","article-title":"On the value of intra-motif dependencies of human insulator protein CTCF","volume":"9","author":"Eggeling","year":"2014","journal-title":"PLOS ONE"},{"key":"2023013108353643800_btz507-B2","doi-asserted-by":"crossref","first-page":"580.","DOI":"10.1093\/bioinformatics\/btw689","article-title":"InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites","volume":"33","author":"Eggeling","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013108353643800_btz507-B3","doi-asserted-by":"crossref","first-page":"2676","DOI":"10.1093\/bioinformatics\/bty158","article-title":"CMV: visualization for RNA and protein family models and their comparisons","volume":"34","author":"Eggenhofer","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013108353643800_btz507-B4","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023013108353643800_btz507-B5","doi-asserted-by":"crossref","first-page":"D335","DOI":"10.1093\/nar\/gkx1038","article-title":"Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families","volume":"46","author":"Kalvari","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023013108353643800_btz507-B6","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1093\/nar\/gkv577","article-title":"Varying levels of complexity in transcription factor binding motifs","volume":"43","author":"Keilwagen","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023013108353643800_btz507-B7","doi-asserted-by":"crossref","first-page":"e1003214.","DOI":"10.1371\/journal.pcbi.1003214","article-title":"The next generation of transcription factor binding site prediction","volume":"9","author":"Mathelier","year":"2013","journal-title":"PLOS Comput Biol"},{"key":"2023013108353643800_btz507-B8","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":"2023013108353643800_btz507-B9","doi-asserted-by":"crossref","first-page":"6055","DOI":"10.1093\/nar\/gkw521","article-title":"Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences","volume":"44","author":"Siebert","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013108353643800_btz507-B10","doi-asserted-by":"crossref","first-page":"2997","DOI":"10.1093\/nar\/10.9.2997","article-title":"Use of the \u2019perceptron\u2019 algorithm to distinguish translational initiation sites","volume":"10","author":"Stormo","year":"1982","journal-title":"Nucleic Acids Res"},{"key":"2023013108353643800_btz507-B11","doi-asserted-by":"crossref","first-page":"5","DOI":"10.32614\/RJ-2011-002","article-title":"testthat: get started with testing","volume":"3","author":"Wickham","year":"2011","journal-title":"R J"},{"key":"2023013108353643800_btz507-B12","doi-asserted-by":"crossref","first-page":"W389","DOI":"10.1093\/nar\/gki439","article-title":"enoLOGOS: a versatile web tool for energy normalized sequence logos","volume":"33","author":"Workman","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023013108353643800_btz507-B13","doi-asserted-by":"crossref","first-page":"17021","DOI":"10.1038\/srep17021","article-title":"Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli","volume":"5","author":"Yang","year":"2015","journal-title":"Sci Rep"},{"key":"2023013108353643800_btz507-B14","doi-asserted-by":"crossref","first-page":"269.","DOI":"10.1186\/s12859-017-1680-2","article-title":"Circularlogo: a lightweight web application to visualize intra-motif dependencies","volume":"18","author":"Ye","year":"2017","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz507\/28894225\/btz507.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4812\/48978326\/bioinformatics_35_22_4812.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4812\/48978326\/bioinformatics_35_22_4812.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,17]],"date-time":"2023-09-17T12:07:18Z","timestamp":1694952438000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/22\/4812\/5521622"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,6,21]]},"references-count":14,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz507","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,11,15]]},"published":{"date-parts":[[2019,6,21]]}}}