{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T06:09:54Z","timestamp":1769234994800,"version":"3.49.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1515,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.<\/jats:p>\n               <jats:p>Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.<\/jats:p>\n               <jats:p>Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http:\/\/www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http:\/\/biojava.org\/wiki\/BioJava:MailingLists<\/jats:p>\n               <jats:p>Contact: andreas.prlic@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts494","type":"journal-article","created":{"date-parts":[[2012,8,12]],"date-time":"2012-08-12T00:24:10Z","timestamp":1344731050000},"page":"2693-2695","source":"Crossref","is-referenced-by-count":158,"title":["BioJava: an open-source framework for bioinformatics in 2012"],"prefix":"10.1093","volume":"28","author":[{"given":"Andreas","family":"Prli\u0107","sequence":"first","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 3Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA, 4College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK, 5Department of Computer Science, University of Wisconsin-Madison, WI 53706, USA, 6Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 7NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597, Singapore, 8Genetics and Genomics Medicine of Inflammation, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8, 9Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK, 10Faculty of Mathematics and Informatics, Vilnius University, LT-03225 Vilnius, Lithuania, 11Harbinger Partners, Inc., St Paul, MN 55127, USA, 12University of Applied Sciences Upper Austria, 4232 Hagenberg, Austria, 13Skaggs"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Yates","sequence":"additional","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 3Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA, 4College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK, 5Department of Computer Science, University of Wisconsin-Madison, WI 53706, USA, 6Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 7NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597, Singapore, 8Genetics and Genomics Medicine of Inflammation, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8, 9Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK, 10Faculty of Mathematics and Informatics, Vilnius University, LT-03225 Vilnius, Lithuania, 11Harbinger Partners, Inc., St Paul, MN 55127, USA, 12University of Applied Sciences Upper Austria, 4232 Hagenberg, Austria, 13Skaggs"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Spencer E.","family":"Bliven","sequence":"additional","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, 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13Skaggs"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter W.","family":"Rose","sequence":"additional","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 3Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA, 4College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK, 5Department of Computer Science, University of Wisconsin-Madison, WI 53706, USA, 6Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, 7NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597, Singapore, 8Genetics and Genomics Medicine of Inflammation, Montreal Heart Institute, Montreal, Quebec, Canada H1T 1C8, 9Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK, 10Faculty of Mathematics and Informatics, Vilnius 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