stuartmac/jabaws repository overview

⁠JABAWS: Bioinformatics Web Services for Alignment and Analysis

JABAWS provides a suite of bioinformatics web services for multiple sequence alignment, protein disorder prediction, and conservation analysis — packaged for convenient deployment on your local computer, server, or cluster.

This resource was developed by the Dundee Resource for Sequence Analysis and Structure Prediction⁠. For more information or to use the public JABAWS server, visit the JABAWS web server⁠.

⁠🚀 Quick Start

Ensure Docker is installed on your system. If needed, refer to the Docker install docs⁠.

In a terminal, run the JABAWS Docker image:

docker run --rm -p 8080:8080 stuartmac/jabaws:latest

This command will download and start the JABAWS web server on your computer and expose the application via localhost:8080

⁠Access the Services

Once started, JABAWS services will be available at:

URL: http://localhost:8080/jabaws/⁠

Open http://localhost:8080/jabaws/ServiceStatus in your web browser to see the service list and status. Services are accessible via Jalview⁠ or the JABAWS CLI⁠.

⁠Use with Jalview 2.11

To enable Jalview to use your local JABAWS instance:

• In Jalview, open Preferences → Web Services, and add your server’s JABAWS URL (e.g., http://localhost:8080/jabaws/)
• Run the tools via the Jalview Web Services menu.

⁠Services Provided

Multiple Sequence Alignment

• Clustal Omega
• Clustal W
• MAFFT
• MUSCLE
• T-Coffee
• ProbCons
• MSAProbs
• GLProbs

Disorder Prediction

• DisEMBL
• IUPred
• Jronn
• GlobPlot

Conservation Analysis

• AACon (v1.1)⁠

RNA Structure Prediction

• RNAalifold (from the Vienna RNA package)

⁠Use Cases

The JABAWS Docker Image is ideal for users needing to:

• Run jobs that exceed our public server limits
• Adhere to strict data policies when working with sensitive data
• Work offline

⁠Slivka

From Jalview 2.12, JABAWS web services will be replaced by Slivka⁠. Please see our slivka-bio Docker repository⁠ for setup and configuration instructions.

Users looking to host bioinformatics web services for programmatic access only (e.g. via Jupyter Notebooks) are recommended to use Slivka.

⁠Funding

This work is part of the BBSRC⁠ funded Dundee Resource for Protein Structure Prediction and Sequence Analysis⁠ grant number 208391/Z/17/Z⁠.