**OutputFolderName**
The folder where the output files are stored.
**genebank_annotations.tsv**
Final tsv file with all the annotations from the Genbank and IDs to add.
What is left after the cleanup.
genbank_annotations
Folder containing Genbank annotations.
genebank_annotations.tsv
file with all the annotations from the Genbank and IDs to add.
best_annotations_all_genbank_files
Folder containing the best Genbank annotations.
best_genbank_annotations.tsv
Best Genbank annotations.
best_annotations_per_genbank_file
Folder containing the best Genbank annotations per file.
genbank_file_x_annotations.tsv
Genbank file x annotations.
genbank_file_y_annotations.tsv
Genbank file y annotations.
...
Other Genbank file annotations.
blast_processing
Folder containing BLASTp database, BLASTp output files, and translation files.
selected_genbank_proteins.fasta
Selected Genbank proteins.
blast_db
Folder containing the BLASTp database.
blast_db_protein.pdb
Position-specific Data Base file.
blast_db_protein.phr
Protein Header Record file.
blast_db_protein.pin
Protein Index file.
blast_db_protein.pog
Protein Organism Group file.
blast_db_protein.pos
Protein Organism Sequence file.
blast_db_protein.pot
Protein Organism Taxonomy file.
blast_db_protein.psq
Protein Sequence Query file.
blast_db_protein.ptf
Protein Taxonomy File.
blast_db_protein.pto
Protein Taxonomy Organism file.
blastp_results
Folder containing BLASTp results.
blast_results_x.tsv
BLAST results for x.
blast_results_y.tsv
BLAST results for y.
...
Other BLAST results.
self_score_folder
Folder containing self-score results.
blast_results_x.tsv
BLAST results for x.
blast_results_y.tsv
BLAST results for y.
...
Other BLAST results.
reps_translations
Folder containing translations.
x_translation.fasta
Translation for x.
y_translation.fasta
Translation for y.
...
Other translations.
**matched_annotations.tsv**
Final file containing all annotations from the match schema option.
What is left after cleanup.
**uniprot_annotations.tsv**
Final file containing all the UniProt annotations.
What is left after cleanup.
uniprot_annotations
Folder containing UniProt annotations.
best_proteomes_annotations_swiss_prot.tsv
Best annotations for Swiss-Prot proteomes.
best_proteomes_annotations_trEMBL.tsv
Best annotations for TrEMBL proteomes.
proteome_matcher_output
Folder containing proteome matcher output.
best_annotations_per_proteome_file
Folder containing the best annotations per proteome file.
Swiss-Prot
Folder containing Swiss-Prot annotations.
proteome_file_x_Swiss-Prot_annotations.tsv
Swiss-Prot annotations for proteome file x.
proteome_file_y_Swiss-Prot_annotations.tsv
Swiss-Prot annotations for proteome file y.
...
Other Swiss-Prot annotations.
TrEMBL
Folder containing TrEMBL annotations.
proteome_file_x_TrEMBL_annotations.tsv
TrEMBL annotations for proteome file x.
proteome_file_y_TrEMBL_annotations.tsv
TrEMBL annotations for proteome file y.
...
Other TrEMBL annotations.
reps_translations
Folder containing translations.
x_translation.fasta
Translation for x.
y_translation.fasta
Translation for y.
...
Other translations.
self_score_folder
Folder containing self-score results.
blast_results_x.tsv
BLAST results for x.
blast_results_y.tsv
BLAST results for y.
...
Other BLAST results.
swiss_prots_processing
Folder containing Swiss-Prot processing results.
blast_processing
Folder with the files of the Blast database and the BLASTp results.
swiss_prots.fasta
Swiss-Prot protein sequences.
swiss_prots_annotations.tsv
Swiss-Prot annotations.
trembl_prots_processing
Folder containing TrEMBL processing results.
blast_processing
Folder with the files of the Blast database and the BLASTp results.
trembl_prots.fasta
TrEMBL protein sequences.
trembl_prots_annotations.tsv
TrEMBL annotations.
Proteomes
Folder containing the zipped fasta files of each proteome.
Proteome_x.fasta.gz
Fasta file with the sequence of the proteome x.
split_proteomes
folder with the files with all the sequences for each database.
prots_descriptions
File with the information of each sequence.
swiss_prot.fasta
File with all the proteome sequences that are from the Swiss-Prot database.
trembl_prot.fasta
File with all the proteome sequences that are from the TrEMBL database.
**consolidated_annotations**
Final file containing all the annotations of the inputs in a single file.