Using self-similarity to analyse protein repeats

Discovery and Analysis of Repeat and Low-Complexity Architectures in Proteins and Their Conserved Evolutionary Relationships Using Self-Homology Dot Plots

Maria W. Górna, Matthew Merski

Methods Mol Biol (2025) 2870:95-116. https://doi.org/10.1007/978-1-0716-4213-9_7

Maria and Matt provide a protocol on the use of our DOTTER-based method (published earlier in BMC Bioinformatics 2020) for analysis of protein repeats. A lot of practical tips were enclosed in this chapter - we hope this makes implementation easier for users!
Using this method which is based on a self-similarity score rather than sequence, we have described previously undetected repeats in multiple protein families - ThDP enzymes, patatins, HtrA proteases and more.