Muscle WS (jabaws)

Muscle WS (jabaws) provides multiple sequence alignment services via the JABAWS web services framework for comparative sequence analysis.

Key Features:

• Multiple Sequence Alignment Methods: Supports ProbCons, T-Coffee, Muscle, MAFFT, and ClustalW for generating multiple sequence alignments.
• Web Services Framework: Implements the JABAWS web services framework and integrates with the Jalview multiple sequence analysis workbench.
• Deployment Flexibility: Can be deployed as a Virtual Appliance (VA) or as a Web Application Archive (WAR) and configured to run on single computers or clusters managed by Grid Engine or LSF.
• Parameter Customization: Exposes application-specific parameters and allows administrators to define named parameter preset combinations and execution limits via configuration files.
• Integration Capabilities: Provides a JABAWS command-line client to integrate services into scripts and automated workflows.

Scientific Applications:

• Comparative Genomics: Produces sequence alignments used to compare homologous regions across genomes.
• Evolutionary Biology: Generates alignments that support evolutionary and comparative analyses.
• Protein Structure Prediction: Supplies multiple sequence alignments used as input for protein structure prediction workflows.

Methodology:

Performs multiple sequence alignment using ProbCons, T-Coffee, Muscle, MAFFT, and ClustalW via the JABAWS web services; supports configuration through configuration files with named presets and execution limits; can be deployed as a Virtual Appliance or WAR and executed on clusters using Grid Engine or LSF; integrates with Jalview and via the JABAWS command-line client.