{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:58:54Z","timestamp":1792133934452,"version":"4.4.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T00:00:00Z","timestamp":1738368000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["RGP0021\/2018"],"award-info":[{"award-number":["RGP0021\/2018"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["National Institutes of Health"],"award-info":[{"award-number":["National Institutes of Health"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["R35GM130376"],"award-info":[{"award-number":["R35GM130376"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA sequence and shape readout represent different modes of protein\u2013DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The DNAdesign webserver and documentation are freely accessible at https:\/\/dnadesign.usc.edu.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf052","type":"journal-article","created":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T05:30:46Z","timestamp":1738387846000},"source":"Crossref","is-referenced-by-count":2,"title":["DNAdesign: feature-aware <i>in silico<\/i> design of synthetic DNA through mutation"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-0712-023X","authenticated-orcid":false,"given":"Yingfei","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1015-5263","authenticated-orcid":false,"given":"Jinsen","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-6557","authenticated-orcid":false,"given":"Tsu-Pei","family":"Chiu","sequence":"additional","affiliation":[{"name":"Department of Quantitative and Computational Biology, University of Southern 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