What is a meaningful representation of protein sequences?

This repository contains code to reproduce the results reported in the following preprint:

What is a meaningful representation of protein sequences? NS Detlefsen, S Hauberg, W Boomsma - arXiv preprint arXiv:2012.02679, 2020

Table 1, Table 2 and Figure 2

See tape subdirectory, containing a fork of the original TAPE code with our modifications.

Figure 3,4,5, and 8

distances.ipynb jupyter notebook (launch in colab)

Figure 6 and 7

blat_class_A1A2_experiments.ipynb jupyter notebook (launch in colab)