JABAWS

JABAWS provides web services to deploy and execute multiple sequence alignment methods (Probcons, T-coffee, Muscle, MAFFT, ClustalW) and integrate them into bioinformatics analysis workflows.

Key Features:

• Multiple Sequence Alignment Services: Exposes Probcons, T-coffee, Muscle, MAFFT, and ClustalW as callable web services for sequence alignment tasks.
• Integration with Jalview Workbench: Integrates with the Jalview multiple sequence analysis workbench to enable direct access to JABAWS services from Jalview.
• Flexible Deployment Options: Deployable as a Virtual Appliance for virtualization platforms (e.g., VMware, Oracle VirtualBox) or as a WAR file for application servers and cluster environments using Grid Engine or LSF with DRMAA.
• Customizable Configuration: Uses simple configuration files to specify named parameter presets and execution limits for each application.
• Command-Line Client Integration: Provides a command-line client for scripting and incorporation of JABAWS services into automated workflows.

Scientific Applications:

• Comparative Genomics: Generates multiple sequence alignments used in comparative analyses of genomic sequences.
• Phylogenetic Analysis: Produces alignments that serve as input for phylogenetic inference and evolutionary studies.
• Protein Structure Prediction: Supplies sequence alignments for homology-based protein structure prediction workflows.
• Sequence Analysis Integration: Enhances sequence analysis workflows through integration with Jalview for visualization and downstream analyses.

Methodology:

Wraps Probcons, T-coffee, Muscle, MAFFT, and ClustalW as web services; deployable as a Virtual Appliance or WAR; supports execution on clusters via Grid Engine and LSF using DRMAA; configurable via plain configuration files; includes a command-line client.