tobsecret / Bokeh_genome_explorer

This is my first Bokeh server app. I built it to help me visualize some underlying properties of bacterial genomes.

Bokeh_genome_explorer

This is my first Bokeh server app.

Here is what it does:

1. loads up a fasta file with coding sequences (DNA) and a whole genome (DNA)
2. calculates the z-score-normalized codon distribution in all coding sequences
3. applies PCA to the dataframe with the codon distributions
4. plots a scatter plot of the PCA data
5. serves the codon distribution of a single selected data point in form of a bar diagram
6. calculates the melting temperature of chunks of the genome and plots a ring plot, colored accordingly.

If you make a copy of the environment in which I worked on this app, you can run bokeh serve genome_codon_usage_app.py --show in the directory to which you cloned the app.

That should give you something like the screenshot below in which I used the zoom tool to zoom in a little bit and marked a single point.