SCRMshaw: supervised cis-regulatory module prediction for insect genomes v1

As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation of their regulatory component. SCRMshaw is a computational tool designed to predict cis-regulatory modules (CRMs) in the genomes of various insect species (Kantorovitz 2009; Kazemian 2011; Asma and Halfon 2019; Asma 2024). One of the key advantages of SCRMshaw is its accessibility. It requires minimal resources—just a genome sequence and training data from known Drosophila CRMs, which are readily available for download. Even users with modest computational skills can run SCRMshaw on a desktop computer for basic applications, although an HPC cluster is recommended for optimal results. SCRMshaw can be tailored to specific needs. Users can employ a single set of training data to predict CRMs associated with a particular gene expression pattern, or utilize multiple sets to provide a rough regulatory annotation for a newly-sequenced genome. This protocol provides an update to the protocol in Kazemian and Halfon (2019) and incorporates modifications introduced in Asma and Halfon (2019) and Asma et al. (2024).