{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:14:11Z","timestamp":1792638851609,"version":"4.5.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1964,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and\/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts.<\/jats:p>\n               <jats:p>Availability and Implementation: JABAWS 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:p>Contact: \u00a0g.j.barton@dundee.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr304","type":"journal-article","created":{"date-parts":[[2011,5,19]],"date-time":"2011-05-19T02:22:22Z","timestamp":1305771742000},"page":"2001-2002","source":"Crossref","is-referenced-by-count":184,"title":["Java bioinformatics analysis web services for multiple sequence alignment\u2014JABAWS:MSA"],"prefix":"10.1093","volume":"27","author":[{"given":"Peter V.","family":"Troshin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B.","family":"Procter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoffrey J.","family":"Barton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,5,18]]},"reference":[{"key":"2023012712455443000_B1","doi-asserted-by":"crossref","first-page":"W689","DOI":"10.1093\/nar\/gkq394","article-title":"BioCatalogue: a universal catalogue of web services for the life sciences","volume":"38","author":"Bhagat","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012712455443000_B2","doi-asserted-by":"crossref","first-page":"W197","DOI":"10.1093\/nar\/gkn238","article-title":"The Jpred 3 secondary structure prediction server","volume":"36","author":"Cole","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012712455443000_B3","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: probabilistic consistency-based multiple sequence alignment","volume":"15","author":"Do","year":"2005","journal-title":"Genome Res."},{"key":"2023012712455443000_B4","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012712455443000_B5","doi-asserted-by":"crossref","first-page":"W729","DOI":"10.1093\/nar\/gkl320","article-title":"Taverna: a tool for building and running workflows of services","volume":"34","author":"Hull","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012712455443000_B6","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bib\/bbn013","article-title":"Recent developments in the MAFFT multiple sequence alignment program","volume":"9","author":"Katoh","year":"2008","journal-title":"Brief. Bioinformat."},{"key":"2023012712455443000_B7","first-page":"709","article-title":"Design and evaluation of Opal2: a toolkit for scientific software as a service","volume-title":"Services - I, 2009 World Conference on Services","author":"Krishnan","year":"2009"},{"key":"2023012712455443000_B8","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012712455443000_B9","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023012712455443000_B10","article-title":"Soaplab2: more reliable Sesame door to bioinformatics programs","volume-title":"The 9th Annual Bioinformatics Open Source Conference.","author":"Senger","year":"2008"},{"key":"2023012712455443000_B11","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2001\/48933300\/bioinformatics_27_14_2001.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/2001\/48933300\/bioinformatics_27_14_2001.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:38:41Z","timestamp":1674826721000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/14\/2001\/194517"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,18]]},"references-count":11,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2011,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr304","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,7]]},"published":{"date-parts":[[2011,5,18]]}}}