{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,23]],"date-time":"2025-08-23T05:24:01Z","timestamp":1755926641061,"version":"3.40.5"},"reference-count":24,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T00:00:00Z","timestamp":1644451200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ANID Millennium Science Initiative Program","award":["NCN19_168"],"award-info":[{"award-number":["NCN19_168"]}]},{"name":"ANID Fondecyt","award":["11140869"],"award-info":[{"award-number":["11140869"]}]},{"name":"ANID Fondequip","award":["EQM160063"],"award-info":[{"award-number":["EQM160063"]}]},{"name":"ANID Doctoral fellowship","award":["21200775"],"award-info":[{"award-number":["21200775"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Is it possible to learn and create a first Hidden Markov Model (HMM) without programming skills or understanding the algorithms in detail? In this concise tutorial, we present the HMM through the 2 general questions it was initially developed to answer and describe its elements. The HMM elements include variables, hidden and observed parameters, the vector of initial probabilities, and the transition and emission probability matrices. Then, we suggest a set of ordered steps, for modeling the variables and illustrate them with a simple exercise of modeling and predicting transmembrane segments in a protein sequence. Finally, we show how to interpret the results of the algorithms for this particular problem. To guide the process of information input and explicit solution of the basic HMM algorithms that answer the HMM questions posed, we developed an educational webserver called HMMTeacher. Additional solved HMM modeling exercises can be found in the user\u2019s manual and answers to frequently asked questions. HMMTeacher is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/hmmteacher.mobilomics.org\/\" xlink:type=\"simple\">https:\/\/hmmteacher.mobilomics.org<\/jats:ext-link>, mirrored at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/hmmteacher1.mobilomics.org\/\" xlink:type=\"simple\">https:\/\/hmmteacher1.mobilomics.org<\/jats:ext-link>. A repository with the code of the tool and the webpage is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/gitlab.com\/kmilo.f\/hmmteacher\" xlink:type=\"simple\">https:\/\/gitlab.com\/kmilo.f\/hmmteacher<\/jats:ext-link>.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009703","type":"journal-article","created":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T18:26:18Z","timestamp":1644517578000},"page":"e1009703","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Hidden Markov Modeling with HMMTeacher"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9971-2280","authenticated-orcid":true,"given":"Camilo","family":"Fuentes-Beals","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2345-5510","authenticated-orcid":true,"given":"Alejandro","family":"Vald\u00e9s-Jim\u00e9nez","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7633-2365","authenticated-orcid":true,"given":"Gonzalo","family":"Riadi","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,2,10]]},"reference":[{"key":"pcbi.1009703.ref001","first-page":"1","author":"B Schuster-B\u00f6ckler","year":"2007","journal-title":"An Introduction to Hidden Markov Models. 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