Tools
Central to Arc’s mission is not only developing state-of-the-art technologies, but also making them widely available to accelerate biomedical research across the globe. At Arc’s Tools Portal, we’re sharing our growing list of computational tools developed by Arc scientists, along with supporting publications, documentation, and code.
Check back often, as we’ll be posting new tools as they are launched, and feel free to contact us at tools@arcinstitute.org with any questions.
Software & Tools
Machine Learning Tools
Evo is a biological foundation model capable of generative design from molecular to genome scale at single-nucleotide resolution.
Published November 2024, Science
Genome Engineering Tools
This tool designs bridge RNA sequences for recombining user-defined target and donor DNA sites using the IS621 bridge recombination system.
Perry et al., Nature, 2024
Built from the largest Cas13d knockdown dataset to date, Arc's deep learning-powered Cas13d Guide RNA Selection Tool nominates high-efficiency guide sequences and any custom RNA sequences for knocking down your transcript of interest across human, mouse, other model organisms, and custom sequences.
Wei et al,. Cell Systems, 2023
Gene Expression Tools
Analysis of alternative poly-A site selection and processing using 3‘-end RNA sequencing.
Nature Cell Biology, May 2023
Discovery of RNA structural elements using in silico and hybrid RNA SHAPE strategies.
Science, May 2021
Ribosome footprinting pre-processing, QC, and analysis.
Nature Cell Biology, May 2023
A tool designed for the systematic discovery of RNA structural switches within transcriptomes.
Nature Methods, July 2024
Atlases
A shiny app for exploration of the Goodarzi lab’s RBP post-transcriptional regulatory modules.
Preprint, March 2023