https://github.com/gamcil/5_utr_analysis
https://github.com/gamcil/5_utr_analysis
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/gamcil/5_utr_analysis
- Owner: gamcil
- License: mit
- Created: 2020-01-09T02:57:09.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-01-09T03:57:23.000Z (over 6 years ago)
- Last Synced: 2025-05-07T20:14:41.305Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 10.7 MB
- Stars: 1
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 5_UTR_analysis
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
## Data
All analysis was performed using version 46 of the *A. nidulans* FGSC A4 genome
obtained from [FungiDB](https://fungidb.org/common/downloads/Current_Release/AnidulansFGSCA4/)
(FungiDB-46_AnidulansFGSCA4_Genome.fasta and FungiDB-46_AnidulansFGSCA4.gff).
## File summary
| 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](https://mycocosm.jgi.doe.gov/pages/sm-clusters.jsf?organism=Aspnid1&genomes=Aspnid1&clusterTypes=DMAT%2CHYBRID%2CNRPS%2CNRPS-Like%2CPKS%2CPKS-Like%2CTC&pageSize=50) |