Predicting gene sequences with AI to study codon usage patterns
with Tomer Sidi, Shiri Bahiri-Elitzur, and Tamir Tuller
We developed and trained an mBART model to predict codon sequences used by an organism to encode a given amino acid sequence. Our models improve upon frequency-based predictions using contemporary AI tools that learn complex patterns and capture interactions between codons.
CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers
with Sergey Nepomnyachiy, and Nir Ben-Tal
CyToStruct is a Cytoscape app that allows the user to configure scripts for running external programs. These scripts are templates, and CyToStruct will inject node/edge dependent data into these and then pass the script on to external programs. The application we had in mind was running molecular viewers that show the details of nodes and edges. Because CyToStruct is so general, we can support any molecular viewer (our demos include four).
code | install | documentation
VISTAL - A two-dimensional visualization tool for structural alignments
with Barry Honig
VISTAL describes structures as a series of secondary structure elements, and places matched residues one on top of each other colored according to the three-dimensional distance of their Ca atoms.