PolyX2: Fast Detection of Homorepeats in Large Protein Datasets

Abstract

Homorepeat sequences, consecutive runs of identical amino acids, are prevalent in eukaryotic proteins. It has become necessary to annotate and evaluate this feature in entire proteomes. The definition of what constitutes a homorepeat is not fixed, and different research approaches may require different definitions; therefore, flexible approaches to analyze homorepeats in complete proteomes are needed. Here, we present polyX2, a fast, simple but tunable script to scan protein datasets for all possible homorepeats. The user can modify the length of the window to scan, the minimum number of identical residues that must be found in the window, and the types of homorepeats to be found.