Classi cation of protein sequences is one big task in bioinformatics and has many applications. Di erent machine learning methods exist and are applied on these problems, such as support vector machines (SVM), random forests (RF), and neural networks (NN). All of these methods have in common that protein sequences have to be made machinereadable and comparable in the rst step, for which di erent encodings exist. ese encodings are typically based on physical or chemical properties of the sequence. However, due to the outstanding performance of deep neural networks (DNN) on image recognition, we used frequency matrix chaos game representation (FCGR) for encoding of protein sequences into images. In this study, we compare the performance of SVMs, RFs, and DNNs, trained on FCGR encoded protein sequences. While the original chaos game representation (CGR) has been used mainly for genome sequence encoding and classi cation, we modi ed it to work also for protein sequences, resulting in n-akes representation, an image with several icosagons. We could show that all applied machine learning techniques (RF, SVM, and DNN) show promising results compared to the state-of-the-art methods on our benchmark datasets, with DNNs outperforming the other methods and that FCGR is a promising new encoding method for protein sequences.