{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:34:22Z","timestamp":1778636062747,"version":"3.51.4"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,6,28]],"date-time":"2019-06-28T00:00:00Z","timestamp":1561680000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/www.compgen.org\/tools\/juchmme, https:\/\/github.com\/pbagos\/juchmme.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz533","type":"journal-article","created":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T18:40:38Z","timestamp":1561488038000},"page":"5309-5312","source":"Crossref","is-referenced-by-count":6,"title":["JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis"],"prefix":"10.1093","volume":"35","author":[{"given":"Ioannis A","family":"Tamposis","sequence":"first","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics , University of Thessaly, Lamia, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5280-1107","authenticated-orcid":false,"given":"Konstantinos D","family":"Tsirigos","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Section for Bioinformatics , Technical University of Denmark, Kgs Lyngby, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margarita C","family":"Theodoropoulou","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics , University of Thessaly, Lamia, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panagiota I","family":"Kontou","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics , University of Thessaly, Lamia, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios N","family":"Tsaousis","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Genekor Medical SA , Athens, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1972-8865","authenticated-orcid":false,"given":"Dimitra","family":"Sarantopoulou","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine and Therapeutics, University of Pennsylvania , Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zoi I","family":"Litou","sequence":"additional","affiliation":[{"name":"Section of Cell Biology and Biophysics, Department of Biology , School of Science, National and Kapodistrian University of Athens, Athens, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4935-2325","authenticated-orcid":false,"given":"Pantelis G","family":"Bagos","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics , University of Thessaly, Lamia, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,28]]},"reference":[{"key":"2023013108374080500_btz533-B1"},{"key":"2023013108374080500_btz533-B2","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1471-2105-5-29","article-title":"A Hidden Markov Model method, capable of predicting and discriminating \u03b2-barrel outer membrane proteins","volume":"5","author":"Bagos","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023013108374080500_btz533-B3","doi-asserted-by":"crossref","first-page":"189.","DOI":"10.1186\/1471-2105-7-189","article-title":"Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins","volume":"7","author":"Bagos","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013108374080500_btz533-B4","doi-asserted-by":"crossref","first-page":"5082","DOI":"10.1021\/pr800162c","article-title":"Prediction of lipoprotein signal peptides in Gram-positive bacteria with a hidden Markov model","volume":"7","author":"Bagos","year":"2008","journal-title":"J. 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