This notebook performs pairwise protein structural alignments using the US-align algorithm by Zhang et al., (2022), then constructs a structure-informed dendrogram using the UPGMA algorithm to visualise similarities.
ColabAlign is designed to run directly in Google Colab for ease-of-use and to remove any local hardware requirements. This implementation also includes multiprocessing support for dramatically increased performance over the base US-align program.
MView uses an expanded character set to represent groups of amino acids with similar properties. Below is Further information can be found at: https://desmid.github.io/mview/manual/manual.html
| Group | MView character | 1 letter amino acid codes |
|---|---|---|
| Alcohol | o |
S, T |
| Aliphatic | l |
I, L, V |
| Aromatic | a |
F, H, W, Y |
| Charged | c |
D, E, H, K, R |
| Hydrophobic | h |
A, C, F, G, H, I, K, L, M, R, T, V, W, Y |
| Negative | - |
D, E |
| Polar | p |
C, D, E, H, K, N, Q, R, S, T |
| Positive | + |
H, K, R |
| Small | s |
A, C, D, G, N, P, S, T, V |
| Tiny | u |
A, G, S |
| Turn-like | t |
A, C, D, E, G, H, K, N, Q, R, S, T |
| Stop | * |
* |
ColabAlign.py is designed to work for Google Colab and running on local machines. A YAML file is provided for easy installation of dependencies in a Conda environment.
For a Conda virtual environment install, simply create an environment with:
conda env create -f colabalign.yml
Using PIP instead? Since most of the depencencies are Python-based, they can be installed directly:
pip install numpy pandas biopython scipy tqdm
The remaining tools, USalign and BEeM, need to be compiled from source. Please see their respective GitHub repos for more information (https://github.com/pylelab/USalign and https://github.com/kad-ecoli/BeEM/).
You can point ColabAlign at the USalign and BEeM binaries by including these flags:
-b /path/to/BEeM or --beem /path/to/BEeM
and
-u /path/to/USalign or --usalign /path/to/USalign
BibTeX-formatted references for this project and the associated references can be found in colabalign.bib and associated-references.bib.
- ColabAlign (paper): https://doi.org/10.1101/2025.10.06.677802
- ColabAlign (code only): https://doi.org/10.5281/ZENODO.14169501
- BioPython: https://doi.org/10.1093/bioinformatics/btp163
- US-align: https://doi.org/10.1038/s41592-022-01585-1
- TreeCluster: https://doi.org/10.1371/journal.pone.0221068
- MUSTANG: https://doi.org/10.1002/prot.20921
- MView: https://doi.org/10.1093/bioinformatics/14.4.380
- BeEM: https://doi.org/10.1186/s12859-023-05388-9
Note
Permission to use, copy, modify, and distribute this program for any purpose, with or without fee, is hereby granted, provided that the notices on the head, the reference information, and this copyright notice appear in all copies or substantial portions of the Software. It is provided "as is" without express or implied warranty.