Setup

conda env create -f environment.yml
conda activate exon-structure-evolution

Pipeline

1. Download Data

1.1 Download Ensembl genome and annotation:

bash scripts/fetch_GRCh38.115_unmasked.sh

1.2 Download UniProt accession mapping and AlphaFold structures:

bash scripts/fetch_uniprot_accession_mapping_v115_v6.sh
bash scripts/fetch_UP000005640_9606_HUMAN_v6.sh

1.3 Download BioMart mappings:

bash scripts/download_mart_mapping_v115.sh
bash scripts/download_mart_orthologs_v115.sh

2. Build AlphaFold database

python scripts/construct_uniprot_accessions_mapping_db.py

3. Run exonize

Constrained structural search:

bash scripts/exonize_GRCh38.116_80_90_80_const_struct.sh

Relaxed structural search:

bash scripts/exonize_GRCh38.116_80_90_80_relaxed_struct.sh