{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T06:30:27Z","timestamp":1744785027411,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T00:00:00Z","timestamp":1559606400000},"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\/501100004184","name":"Northeastern University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004184","id-type":"DOI","asserted-by":"publisher"}]},{"name":"College of Arts, Media and Design"},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"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>Multiple Sequence Alignments (MSAs) are a fundamental operation in genome analysis. However, MSA visualizations such as sequence logos and matrix representations have changed little since the nineties and are not well suited for displaying large-scale alignments. We propose a novel, web-based MSA visualization tool called NX4, which can handle genome alignments comprising thousands of sequences. NX4 calculates the frequency of each nucleotide along the alignment and visually summarizes the results using a color-blind friendly palette that helps identifying regions of high genetic diversity. NX4 also provides the user with additional assistance in finding these regions with a \u2018focus + context\u2019 mechanism that uses a line chart of the Shannon entropy across the alignment. The tool offers geneticists an easy-to-use and scalable analysis for large MSA studies.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>NX4 is freely available at https:\/\/www.nx4.io, and its source code at https:\/\/github.com\/NX4\/nx4.<\/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\/btz457","type":"journal-article","created":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T11:09:02Z","timestamp":1559214542000},"page":"4800-4802","source":"Crossref","is-referenced-by-count":4,"title":["NX4: a web-based visualization of large multiple sequence alignments"],"prefix":"10.1093","volume":"35","author":[{"given":"A","family":"Solano-Roman","sequence":"first","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"College of Arts, Media + Design, Northeastern University , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C","family":"Cruz-Castillo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Universidad Latina de Costa Rica , San Jos\u00e9 11501, Costa Rica"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D","family":"Offenhuber","sequence":"additional","affiliation":[{"name":"College of Arts, Media + Design, Northeastern University , Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A","family":"Colubri","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,4]]},"reference":[{"year":"2017","author":"Bostock","key":"2023013108355992500_btz457-B1"},{"key":"2023013108355992500_btz457-B2","first-page":"2:1","article-title":"A review of overview+detail, zooming, and focus+context interfaces","volume-title":"ACM Comput. 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