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JABAWS specifications


Unique identifier OMICS_26671
Software type Application/Script
Interface Command line interface, Graphical user interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Version 2.2
Stability Stable
Source code URL http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-src-2.2.0.jar
Maintained Yes



  • person_outline Geoffrey J. Barton

Additional information


Publications for JABAWS

JABAWS citations


A study of the structural properties of sites modified by the O linked 6 N acetylglucosamine transferase

PLoS One
PMCID: 5590929
PMID: 28886091
DOI: 10.1371/journal.pone.0184405

[…] /T was at least 100 residues away from the N- and C-termini to avoid edge effects. The intrinsic disorder was predicted by JRonn (Java implementation of Ronn []), IUPred [] and DisEMBL [] through the JABAWS [] command line application. Between them, these methods provide 6 different disorder prediction scores: DisEMBL-REM465 (0.6), DisEMBL-COILS (0.516), DisEMBL-HOTLOOPS (0.1204), IUPred-Long (0.5 […]


A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii

PMCID: 5487736
PMID: 28655825
DOI: 10.1128/mBio.00950-17
call_split See protocol

[…] re were visualized using UCSF Chimera (). Sequences were aligned using default T-Coffee settings and were viewed through Jalview (). Analysis of the conservation between sequences was performed using JABAWS (). […]


A Proteomic Approach to Analyze the Aspirin mediated Lysine Acetylome*

PMCID: 5294217
PMID: 27913581
DOI: 10.1074/mcp.O116.065219

[…] , or where a prediction takes longer than 1 h will not get a prediction. Thus, a small number of proteins do not get a secondary structure prediction. DisEMBL disorder prediction () was performed via JabaWS (). The central lysine residue for each peptide was then interrogated in its parent protein for its secondary structure and disorder prediction and assigned as being either in helical, beta str […]


Inter locus as well as intra locus heterogeneity in LINE 1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs

Clin Epigenetics
PMCID: 4367886
PMID: 25798207
DOI: 10.1186/s13148-015-0051-y

[…] able gap weighting (speed oriented) method implemented by ClustalWS in the Jalview 2.7 Java-based multiple sequence alignment editor implementing the Java Bioinformatics Analysis Web Services system (JABAWS). The resulting alignment was further manually curated to remove any remaining gaps.The three methods resulted in three different, partly overlapping sequences covering varied numbers of CpGs o […]


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JABAWS institution(s)
Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
JABAWS funding source(s)
Supported by the European Network of Excellence ENFIN [contract LSHG-CT-2005-518254]; UK Biotechnology and Biological Sciences Research Council Grants [BB/J019364/1, BB/L020742/1] and the Scottish Universities Life Sciences Alliance (SULSA).

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