Jronn WS (jabaws)

Jronn WS (jabaws) provides web services to deploy and run multiple sequence alignment algorithms (Probcons, T-coffee, Muscle, Mafft, ClustalW) for sequence analysis and integration into computational workflows.

Key Features:

• Multiple Sequence Alignment Services: Exposes MSA methods Probcons, T-coffee, Muscle, Mafft, and ClustalW via the JABAWS:MSA service.
• Deployment Options: Supports deployment as a Virtual Appliance (VA) for virtualization environments such as VMware or Oracle VirtualBox and as a Web Application Archive (WAR) for execution on single machines or clusters.
• Cluster Integration: WAR deployment supports execution on clusters managed by Grid Engine or LSF and integration with queuing systems via DRMAA.
• Parameter Customization: Provides access to application parameters, named parameter preset combinations, and execution limits configurable through configuration files.
• Command-Line Integration: Includes a command-line client to integrate JABAWS services into scripts and bioinformatics pipelines.
• Scalable Web Services Architecture: Implements web services to provide scalable, flexible access to bioinformatics applications in standalone or clustered environments.

Scientific Applications:

• Phylogenetic Analysis: Generates multiple sequence alignments suitable for phylogenetic reconstruction.
• Protein Structure Prediction: Produces alignments that serve as input for protein structure prediction workflows.
• Functional Annotation: Supports comparative sequence analysis for functional annotation of genes.

Methodology:

Operates via web services to expose MSA applications and supports deployment as a Virtual Appliance (VA) or Web Application Archive (WAR), with WAR capable of running on clusters managed by Grid Engine or LSF using DRMAA.