Supplemental Dataset for: Exonize: a tool for finding and classifying exon duplications in annotated genomes

This dataset contains all the required scripts and data to reproduce the results presented in the article "exonize: a tool for finding and classifying exon duplications in annotated genomes". The dataset comprises the following files: ensembl_eukaryotes_analysis: <specieid>_results.db: Exonize SQLite output for all species included in the analysis. src/fetch_eukaryotes_data.sh: Bash script for downloading genomes and annotations from the Ensembl database (release 114). src/sample.sh: Bash script used to run exonize on each species. src/ensembl_eukaryotes_table.py: Python script to reproduce Table 1 in the main article. local_search_sensitivity_analysis: Homo_sapiens.GRCh38.114.<ce.te.ct*>_results.db: Exonize SQLite output for different parameter settings. src/sample.sh: Bash script to run exonize with specified parameters. src/local_search_sensitivity_analysis_tables.py: Python script to reproduce Table 1 in the Supplementary Information. validation: simulated_data/data/Homo_sapiens.GRCh38.chromosome.Y.mutated.gff3: Simulated annotations (GFF3). simulated_data/data/Homo_sapiens.GRCh38.dna.chromosome.Y.mutated.fa: Simulated DNA sequence (FASTA) simulated_data/data/sim_events.csv: CSV file with the locations of all full-length and intronic simulated events. simulated_data/src/simulation_stats.py: Python script to reproduce Figure 2 in the Supplementary Information. Gomez_et_al_comparison/gencode.v33.80.90.80_results.db: Exonize SQLite output based on human GENCODE v33 annotations (GFF3). Gomez_et_al_comparison/gencode.v33.relaxed_results.db: Exonize SQLite output from a relaxed search on human GENCODE v33 annotations. Gomez_et_al_comparison/data/gencode.v33.annotations.zip: GENCODE v33 annotations (GFF3), including protein-coding genes only. Gomez_et_al_comparison/src/fetch_gencode_data.sh: Bash script for downloading the GENCODE v33 human genome (FASTA). Gomez_et_al_comparison/src/gencode_human_comparison.py: Python script to reproduce Figure 3 in the Supplementary Information. *Note: te refers to query coverage, ce the clustering exon threshold, and ctthe target clustering threshold.