{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:13:58Z","timestamp":1792638838233,"version":"4.5.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,30]],"date-time":"2018-01-30T00:00:00Z","timestamp":1517270400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011105","name":"Fourth Framework Programme","doi-asserted-by":"publisher","award":["LSHG-CT-2005-518254"],"award-info":[{"award-number":["LSHG-CT-2005-518254"]}],"id":[{"id":"10.13039\/100011105","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/J019364\/1"],"award-info":[{"award-number":["BB\/J019364\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/L020742\/1"],"award-info":[{"award-number":["BB\/L020742\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800 000 analyses for users worldwide.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http:\/\/www.compbio.dundee.ac.uk\/jabaws.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty045","type":"journal-article","created":{"date-parts":[[2018,1,29]],"date-time":"2018-01-29T20:12:57Z","timestamp":1517256777000},"page":"1939-1940","source":"Crossref","is-referenced-by-count":77,"title":["JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure"],"prefix":"10.1093","volume":"34","author":[{"given":"Peter V","family":"Troshin","sequence":"first","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B","family":"Procter","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Sherstnev","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel L","family":"Barton","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F\u00e1bio","family":"Madeira","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9014-5355","authenticated-orcid":false,"given":"Geoffrey J","family":"Barton","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,1,30]]},"reference":[{"key":"2023012713560808100_bty045-B1","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-9-474","article-title":"RNAalifold: improved consensus structure prediction for RNA alignments","volume":"9","author":"Bernhart","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012713560808100_bty045-B2","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1093\/bioinformatics\/bti541","article-title":"IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content","volume":"21","author":"Doszt\u00e1nyi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012713560808100_bty045-B3","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1016\/j.str.2003.10.002","article-title":"Protein disorder prediction: implications for structural proteomics","volume":"11","author":"Linding","year":"2003","journal-title":"Structure"},{"key":"2023012713560808100_bty045-B4","doi-asserted-by":"crossref","first-page":"3701","DOI":"10.1093\/nar\/gkg519","article-title":"GlobPlot: exploring protein sequences for globularity and disorder","volume":"31","author":"Linding","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023012713560808100_bty045-B5","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1093\/bioinformatics\/btq338","article-title":"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities","volume":"26","author":"Liu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012713560808100_bty045-B6","doi-asserted-by":"crossref","first-page":"51.","DOI":"10.1186\/1471-2105-9-51","article-title":"The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction","volume":"9","author":"Manning","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012713560808100_bty045-B7","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2014","journal-title":"Mol. 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