Alternative Visualization Methods for CLANS Output: Using Cytoscape or Other Tools

Question

[Rohan]

I'm using CLANS (CLuster ANalysis of Sequences) for 3D visualization of protein clusters based on sequence similarity. CLANS is a Java-based tool that visualizes protein families by performing an all-against-all BLAST search to obtain a similarity matrix, which is then represented in a 2D or 3D graph using the Fruchterman-Reingold force-directed layout algorithm.

https://doi.org/10.1093/bioinformatics/bth444

Although CLANS provides a useful graphical representation of sequence similarities, the tool is relatively old, lags when visualizing large clusters, and primarily doesn't allow too many aesthetic customizations. I'm looking for ways to enhance the visual appeal and aesthetics of the CLANS output. Specifically, I have a few questions:

1. Aesthetic Enhancements: Are there newer methods or tools available that can improve the visual aesthetics of CLANS output? How can we create more polished and publication-quality images from CLANS results?

2. Integration with Cytoscape: Can Cytoscape be used to visualize Fruchterman-Reingold layouts? If so, how can we export CLANS data in a format compatible with Cytoscape, and what steps are involved in creating aesthetically pleasing visualizations within Cytoscape?

3. Alternative Visualization Tools: Besides Cytoscape, are there any other software tools or methods that are particularly effective for visualizing CLANS output or similar sequence similarity networks? What are the best practices for achieving high-quality, visually appealing representations?

Any advice or experiences with enhancing CLANS visualizations or integrating its output with other tools would be greatly appreciated.

Answer 1

[Scooter]

You should take a look at the Enzyme Function Initiative, which is similar to what CLANS does. They use Cytoscape extensively. In fact, the Cytoscape implementation of Fruchterman-Reingold was initially implemented to support sequence similarity networks (it's called BioLayout in Cytoscape). There are other, faster, force-directed layouts in Cytoscape that you may want to try also.

-- scooter

[Rohan]

How can we utilize these tools to produce an output similar to CLANS? Could you please provide a detailed, step-by-step guide?