{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T23:47:31Z","timestamp":1722728851908},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2333,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening\/extension penalties.<\/jats:p>\n               <jats:p>We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications.<\/jats:p>\n               <jats:p>Availability and Implementation: The software is freely available at: http:\/\/melolab.org\/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.<\/jats:p>\n               <jats:p>Contact: All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq252","type":"journal-article","created":{"date-parts":[[2010,5,15]],"date-time":"2010-05-15T00:17:52Z","timestamp":1273882672000},"page":"1664-1665","source":"Crossref","is-referenced-by-count":4,"title":["Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming"],"prefix":"10.1093","volume":"26","author":[{"given":"Ignacio L.","family":"Ibarra","sequence":"first","affiliation":[{"name":"Laboratorio de Bioinform\u00e1tica Molecular, Departamento de Gen\u00e9tica Molecular y Microbiolog\u00eda, Facultad de Ciencias Biol\u00f3gicas, Pontificia Universidad Cat\u00f3lica de Chile, Alameda 340, Santiago, Chile"}]},{"given":"Francisco","family":"Melo","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioinform\u00e1tica Molecular, Departamento de Gen\u00e9tica Molecular y Microbiolog\u00eda, Facultad de Ciencias Biol\u00f3gicas, Pontificia Universidad Cat\u00f3lica de Chile, Alameda 340, Santiago, Chile"}]}],"member":"286","published-online":{"date-parts":[[2010,5,14]]},"reference":[{"key":"2023012507553605800_B1","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1073\/pnas.38.8.716","article-title":"On the theory of dynamic programming","volume":"38","author":"Bellman","year":"1952","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507553605800_B2","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1126\/science.153.3731.34","article-title":"Dynamic programming","volume":"153","author":"Bellman","year":"1966","journal-title":"Science"},{"key":"2023012507553605800_B3","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1017\/CBO9780511790492.003","volume-title":"Biological Sequence Analysis","author":"Durbin","year":"1998","edition":"1st"},{"key":"2023012507553605800_B4","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nbt0704-909","article-title":"What is dynamic programming?","volume":"22","author":"Eddy","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2023012507553605800_B5","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1093\/bioinformatics\/16.1.41","article-title":"The early introduction of dynamic programming into computational biology","volume":"16","author":"Sankoff","year":"2000","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/13\/1664\/48851877\/bioinformatics_26_13_1664.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/13\/1664\/48851877\/bioinformatics_26_13_1664.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:56:03Z","timestamp":1674633363000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/13\/1664\/201588"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,5,14]]},"references-count":5,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2010,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq252","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,7,1]]},"published":{"date-parts":[[2010,5,14]]}}}