{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T18:15:09Z","timestamp":1778868909319,"version":"3.51.4"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T00:00:00Z","timestamp":1707955200000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62136004"],"award-info":[{"award-number":["62136004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62276130"],"award-info":[{"award-number":["62276130"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Development Plan of Jiangsu Province","award":["BE2022842"],"award-info":[{"award-number":["BE2022842"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The main program is available at https:\/\/github.com\/guanxiaoyu11\/S2Inet.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae083","type":"journal-article","created":{"date-parts":[[2024,2,17]],"date-time":"2024-02-17T07:02:13Z","timestamp":1708153333000},"source":"Crossref","is-referenced-by-count":4,"title":["T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence 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Aeronautics and Astronautics , Nanjing 211106, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daoqiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence , Nanjing 211106, China"},{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, Nanjing University of Aeronautics and Astronautics , Nanjing 211106, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,15]]},"reference":[{"key":"2024022909074639100_btae083-B1","doi-asserted-by":"crossref","first-page":"2086","DOI":"10.1529\/biophysj.104.042960","article-title":"Microscopic kinetics of DNA translocation through synthetic nanopores","volume":"87","author":"Aksimentiev","year":"2004","journal-title":"Biophys 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