ClustalO WS (jabaws)

ClustalO WS (jabaws) provides multiple sequence alignment services within the JABAWS framework for sequence analysis.

Key Features:

• Multiple Sequence Alignment Methods: JABAWS:MSA exposes Probcons, T-coffee, Muscle, MAFFT, and ClustalW alignment algorithms.
• Virtual Appliance deployment: Distributed as a Virtual Appliance for deployment in virtualization environments such as VMware and Oracle VirtualBox.
• WAR distribution and cluster integration: Distributed as a Web Application Archive (WAR) for configuration on single computers or clusters managed by Grid Engine or LSF using DRMAA.
• Customizable parameters and execution limits: Administrators can specify named parameter presets and execution limits for each application via configuration files.
• Command-line client: Provides a command-line client to integrate services into automated scripts.

Scientific Applications:

• Phylogenetic analysis: Producing multiple sequence alignments used for phylogenetic inference and evolutionary studies.
• Protein structure prediction: Generating alignments for homology modelling and comparative structure prediction.
• Functional annotation: Creating alignments to support transfer of functional annotations and conserved motif identification.

Methodology:

Implements the JABAWS web services framework, deployable as a Virtual Appliance or WAR, configurable for clusters managed by Grid Engine or LSF via DRMAA, and integrated with the Jalview workbench.