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 Ensembl. 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. ensembl_local_search_sensitivity_analysis: Homo_sapiens.GRCh38.113.<te.ce.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. Gomez_et_al_comparison: gencode.v33.80.90.80_results.db: exonize SQLite output for human GENCODE v33 annotations. src/fetch_gencode_data.sh: Bash script for downloading the GENCODE v33 human genome. src/gencode.v33.annotations.zip: GENCODE v33 annotations, including protein-coding genes only. src/gencode_human_comparison.py: Python script to reproduce Figure 1 in the Supplementary Information. *Note: te refers to query coverage, ce the clustering exon threshold, and ctthe target clustering threshold.