Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

This script identifies homologous, non-overlapping regions within a circular DNA sequence using BLASTn. It’s useful for detecting repeats like transposons or duplicated segments in bacterial genomes or plasmids. I originally wrote this for a friend doing a PhD in molecular microbiology/biotech, but it might be helpful for others as well! :)