JABAWS 2.2 Distributed Web Services for Bioinformatics

Protein Disorder, Conservation and RNA Secondary Structure

Peter V. Troshin, James B. Procter, Alexander Sherstnev, Daniel L. Barton, Fábio Madeira, Geoffrey J. Barton (Lead / Corresponding author)

Research output: Contribution to journalArticle

2 Citations (Scopus)
26 Downloads (Pure)

Abstract

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. Availability and Implementation: JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws.
Original languageEnglish
Article numberbyt045
Pages (from-to)1939-1940
Number of pages2
JournalBioinformatics
Volume34
Issue number11
Early online date30 Jan 2018
DOIs
Publication statusPublished - 1 Jun 2018

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RNA Secondary Structure
Sequence Alignment
Bioinformatics
Computational Biology
RNA
Web services
Web Services
Disorder
Conservation
Multiple Sequence Alignment
Proteins
Protein
Licensure
Servers
Server
Sequence Analysis
Structure Prediction
Line
Web Application
Simplify

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Troshin, Peter V. ; Procter, James B. ; Sherstnev, Alexander ; Barton, Daniel L. ; Madeira, Fábio ; Barton, Geoffrey J. / JABAWS 2.2 Distributed Web Services for Bioinformatics : Protein Disorder, Conservation and RNA Secondary Structure. In: Bioinformatics. 2018 ; Vol. 34, No. 11. pp. 1939-1940.
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abstract = "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. Availability and Implementation: JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws.",
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JABAWS 2.2 Distributed Web Services for Bioinformatics : Protein Disorder, Conservation and RNA Secondary Structure. / Troshin, Peter V. ; Procter, James B.; Sherstnev, Alexander; Barton, Daniel L.; Madeira, Fábio; Barton, Geoffrey J. (Lead / Corresponding author).

In: Bioinformatics, Vol. 34, No. 11, byt045, 01.06.2018, p. 1939-1940.

Research output: Contribution to journalArticle

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