{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T02:53:04Z","timestamp":1769741584769,"version":"3.49.0"},"reference-count":61,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)","award":["LARA\u20142021"],"award-info":[{"award-number":["LARA\u20142021"]}]},{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)","award":["#2013\/07375-0"],"award-info":[{"award-number":["#2013\/07375-0"]}]},{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)","award":["#2021\/08561-8"],"award-info":[{"award-number":["#2021\/08561-8"]}]},{"name":"Universidade de S\u00e3o Paulo (USP)","award":["LARA\u20142021"],"award-info":[{"award-number":["LARA\u20142021"]}]},{"name":"Universidade de S\u00e3o Paulo (USP)","award":["#2013\/07375-0"],"award-info":[{"award-number":["#2013\/07375-0"]}]},{"name":"Universidade de S\u00e3o Paulo (USP)","award":["#2021\/08561-8"],"award-info":[{"award-number":["#2021\/08561-8"]}]},{"name":"S\u00e3o Paulo Research Foundation (FAPESP)","award":["LARA\u20142021"],"award-info":[{"award-number":["LARA\u20142021"]}]},{"name":"S\u00e3o Paulo Research Foundation (FAPESP)","award":["#2013\/07375-0"],"award-info":[{"award-number":["#2013\/07375-0"]}]},{"name":"S\u00e3o Paulo Research Foundation (FAPESP)","award":["#2021\/08561-8"],"award-info":[{"award-number":["#2021\/08561-8"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>In recent years, there has been an exponential growth in sequencing projects due to accelerated technological advances, leading to a significant increase in the amount of data and resulting in new challenges for biological sequence analysis. Consequently, the use of techniques capable of analyzing large amounts of data has been explored, such as machine learning (ML) algorithms. ML algorithms are being used to analyze and classify biological sequences, despite the intrinsic difficulty in extracting and finding representative biological sequence methods suitable for them. Thereby, extracting numerical features to represent sequences makes it statistically feasible to use universal concepts from Information Theory, such as Tsallis and Shannon entropy. In this study, we propose a novel Tsallis entropy-based feature extractor to provide useful information to classify biological sequences. To assess its relevance, we prepared five case studies: (1) an analysis of the entropic index q; (2) performance testing of the best entropic indices on new datasets; (3) a comparison made with Shannon entropy and (4) generalized entropies; (5) an investigation of the Tsallis entropy in the context of dimensionality reduction. As a result, our proposal proved to be effective, being superior to Shannon entropy and robust in terms of generalization, and also potentially representative for collecting information in fewer dimensions compared with methods such as Singular Value Decomposition and Uniform Manifold Approximation and Projection.<\/jats:p>","DOI":"10.3390\/e24101398","type":"journal-article","created":{"date-parts":[[2022,10,8]],"date-time":"2022-10-08T04:04:56Z","timestamp":1665201896000},"page":"1398","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4975-7867","authenticated-orcid":false,"given":"Robson P.","family":"Bonidia","sequence":"first","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos 13566-590, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6791-0768","authenticated-orcid":false,"given":"Anderson P.","family":"Avila Santos","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos 13566-590, Brazil"},{"name":"Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, 04318 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2041-9170","authenticated-orcid":false,"given":"Breno L. S.","family":"de Almeida","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos 13566-590, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, 04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6972-6692","authenticated-orcid":false,"given":"Ulisses","family":"Nunes da Rocha","sequence":"additional","affiliation":[{"name":"Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ GmbH, 04318 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8972-5221","authenticated-orcid":false,"given":"Danilo S.","family":"Sanches","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Federal University of Technology-Paran\u00e1\u2014UTFPR, Corn\u00e9lio Proc\u00f3pio 86300-000, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4765-6459","authenticated-orcid":false,"given":"Andr\u00e9 C. P. L. F.","family":"de Carvalho","sequence":"additional","affiliation":[{"name":"Institute of Mathematics and Computer Sciences, University of S\u00e3o Paulo, S\u00e3o Carlos 13566-590, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1080\/13102818.2017.1364977","article-title":"Intelligent mining of large-scale bio-data: Bioinformatics applications","volume":"32","author":"Hashemi","year":"2018","journal-title":"Biotechnol. Biotechnol. 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