exon-structure-evolution

Pipeline

1. Download data

1.1 Ensembl human genome and gff3 annotation v115:

bash scripts/fetch/fetch_GRCh38.115_unmasked.sh

1.2 UniProt accession mapping and AlphaFold structures:

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

1.3 Human canonical transcript mapping from BioMart:

bash scripts/fetch/fetch_mart_human_canonical_transcripts_v115.sh

1.4 BioMart ortholog data (21 species):

bash scripts/fetch/fetch_mart_21_species_orthologs_v115.sh

1.5 BioMart paralog data (21 species):

bash scripts/fetch/fetch_mart_21_species_paralogs_v115.sh

1.6 Pext score annotations:

bash scripts/fetch/fetch_pext_gnomad_v4.1.sh

2. Build databases

UniProt/AlphaFold mapping database:

python scripts/build/build_uniprot_accessions_mapping_db.py

BioMart ortholog database:

python scripts/build/build_biomart_orthologs_db.py

BioMart paralog database:

python scripts/build/build_biomart_human_paralogs_db.py

3. Run exonize

Constrained structural search:

bash scripts/exonize/exonize_GRCh38.116_80_90_80_const_struct.sh

Relaxed structural search:

bash scripts/exonize/exonize_GRCh38.116_80_90_80_relaxed_struct.sh