Code accompanying the paper:
CRISPRa of biosynthetic gene clusters for bioactive molecule discovery in filamentous fungi
Indra Roux, Clara Woodcraft, Jinyu Hu, Rebecca Wolters, Cameron L.M. Gilchrist, Yit-Heng Chooi
All analysis was performed using version 46 of the A. nidulans FGSC A4 genome obtained from FungiDB (FungiDB-46_AnidulansFGSCA4_Genome.fasta and FungiDB-46_AnidulansFGSCA4.gff).
File | Description |
---|---|
notebook.ipynb | Jupyter notebook containing all code used in analyses |
five_prime_UTRs_genome.csv | Summary of 5'UTRs for all genes in A. nidulans |
five_prime_UTRs_bgcs.csv | Summary of 5'UTRs for genes in A. nidulans BGCs |
PAM_per_gene_CDS.svg | Total Cas9/Cas12a PAM sites per gene in all genes/genes in BGCs |
5UTR_length_distribution.svg | Distribution of 5'UTR lengths in all genes/genes in BGCs |
clusters.csv | Predicted BGCs, adapted from A. nidulans portal on JGI |