usum 0.1.1

USUM: Plotting sequence similarity using USEARCH & UMAP

USUM: Plotting sequence similarity using USEARCH & UMAP

USUM uses USEARCH and UMAP to plot DNA 🧬and protein 🧶 sequence similarity embeddings.

Installation

Install UCLUST manually: https://drive5.com/usearch/download.html (consider supporting the author by buying the 64bit license)

Install usum using PIP:

pip install usum

Usage

Minimal example

usum sequences.fa --maxdist 0.2 --termdist 0.3 --output umap

Multiple input files with labels

usum first.fa second.fa --labels First Second --maxdist 0.2 --termdist 0.3 --output umap

This will produce a PNG plot:

An interactive Bokeh HTML plot is also created:

Programmatic use

from usum import usum

# Show help
help(usum)

# Run USUM
usum(inputs=['input.fa'], output='usum', maxdist=0.2, termdist=0.3)

How it works

• A sparse distance matrix is calculated using USEARCH calc_distmx command.
• The distance matrix is embedded as precomputed metric using UMAP
• The embedding is plotted using umap.plot.