GLprobs WS (jabaws)

GLprobs WS (jabaws) provides web-service access via the JABAWS framework to multiple sequence alignment algorithms (Probcons, T-Coffee, Muscle, MAFFT, ClustalW) for generating alignments used in phylogenetic, protein structure and evolutionary analyses.

Key Features:

• Supported algorithms: Executes Probcons, T-Coffee, Muscle, MAFFT and ClustalW for multiple sequence alignment.
• Deployment options: Available as a Virtual Appliance (VA) or Web Application Archive (WAR) and configurable to run on individual machines or clusters managed by Grid Engine, LSF or other DRMAA-compliant queuing systems.
• Configuration management: Administrators can define named parameter presets and set execution limits for each MSA application via configuration files.
• Parameter customization: Clients can specify and modify parameters of each MSA application when submitting alignment jobs.
• Command-line integration: Provides a command-line client to incorporate JABAWS services into scripts and automated workflows.

Scientific Applications:

• Phylogenetic analysis: Produces MSAs used to infer evolutionary relationships and build phylogenetic trees.
• Protein structure prediction: Generates alignments for comparative modelling and identification of conserved structural features.
• Evolutionary biology: Supports analyses of sequence conservation, divergence and evolutionary patterns across homologous sequences.

Methodology:

Implements the Java-based JABAWS framework to execute Probcons, T-Coffee, Muscle, MAFFT and ClustalW; supports deployment as a Virtual Appliance or WAR and integration with Grid Engine, LSF and other DRMAA-compliant queuing systems; uses named parameter presets and execution limits and exposes a command-line client.