Scripts used for the bioinformatic analysis of the paper by Pushkarev, Inoue, et al. 2018. Available at: https://www.nature.com/articles/s41586-018-0225-9 and https://rdcu.be/1ebq
Abundance calculations:
diamond_processing-RPKM.ipynb: Notebook to normalize the abundance of rhodopsins and heliorhodopsins in metagenomes.
Type 1 rhodopsins and heliorhodopsins identity comparison:
blast_heatmap.ipynb: Notebook to compare the blastp identity among type 1 rhodopsins and heliorhodopsins.
The DIAMOND databases used for the metagenomic recruitment can be donwloaded from the following repository: