Quick Start Guide ================ This guide helps you get started with run_dbCAN using example data and explains the generated output files. The tool offers two approaches: 1. **Automated analysis** - Complete workflow with a single command 2. **Step-by-step analysis** - Breaking down the process for troubleshooting or customization Here we performed the `Automated analysis` for each example file. For the `Step-by-step analysis` analysis, please refer to the documentation `user_guide`. Example Data -------------- We provide several example datasets in the `example_data `_ directory for testing purposes. Database Download ------------------ First, download the database files required for the analysis. **Make sure you have installed successfully and activated the `run_dbcan` environment.** .. code-block:: shell # Download database files run_dbcan database \ --db_dir db # Optional: use --aws_s3 for faster and more stable downloads from AWS S3 # run_dbcan database --db_dir db --aws_s3 CAZyme Annotation ------------------ Let's annotate Carbohydrate-Active enZYmes (CAZymes) in our example data. **Example 1: Prokaryotic Genome (DNA)** .. code-block:: shell # Download example prokaryotic genome (E. coli K-12 MG1655) wget -q https://bcb.unl.edu/dbCAN2/download/test/NCBI_prok_test/EscheriaColiK12MG1655.fna -O EscheriaColiK12MG1655.fna # Run CAZyme annotation run_dbcan CAZyme_annotation \ --input_raw_data EscheriaColiK12MG1655.fna \ --mode prok \ --output_dir output_EscheriaColiK12MG1655_fna \ --db_dir db .. _Escherichia coli Strain MG1655: https://www.ncbi.nlm.nih.gov/nuccore/U00096.2 **Example 2: Prokaryotic Proteome (Protein)** .. code-block:: shell # Download example prokaryotic proteome wget -q https://bcb.unl.edu/dbCAN2/download/test/NCBI_prok_test/EscheriaColiK12MG1655.faa -O EscheriaColiK12MG1655.faa # Run CAZyme annotation (specify input format for protein sequences) run_dbcan CAZyme_annotation \ --input_raw_data EscheriaColiK12MG1655.faa \ --mode protein \ --output_dir output_EscheriaColiK12MG1655_faa \ --db_dir db \ **Example 3: Eukaryotic Proteome (NCBI)** .. code-block:: shell # Download example eukaryotic proteome wget -q https://bcb.unl.edu/dbCAN2/download/test/NCBI_euk_test/Xylona_heveae_TC161.faa -O Xylona_heveae_TC161.faa # Run CAZyme annotation run_dbcan CAZyme_annotation \ --input_raw_data Xylona_heveae_TC161.faa \ --mode protein \ --output_dir output_Xylona_heveae_TC161_faa \ --db_dir db .. _Xylona heveae TC161: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001619985.1/ **Example 4: Eukaryotic Proteome (JGI)** .. code-block:: shell # Download example JGI format proteome wget -q https://bcb.unl.edu/dbCAN2/download/test/JGI_test/Xylhe1_GeneCatalog_proteins_20130827.aa.fasta -O Xylhe1_GeneCatalog_proteins_20130827.aa.fasta # Run CAZyme annotation run_dbcan CAZyme_annotation \ --input_raw_data Xylhe1_GeneCatalog_proteins_20130827.aa.fasta \ --mode protein \ --output_dir output_Xylhe1_faa \ --db_dir db .. _Xylhe1: https://mycocosm.jgi.doe.gov/Xylhe1/Xylhe1.home.html CAZyme Annotation Output Files ----------------------------- After running CAZyme annotation, you'll find these output files: ``uniInput.faa`` Unified input file for all tools, generated by Prodigal (for nucleotide input) or provided by the user (for protein input). ``dbCANsub_hmm_results.tsv`` Results from pyHMMER search using dbCAN_sub-HMM database. ``diamond.out`` Results from DIAMOND BLAST search against CAZy database. ``dbCAN_hmm_results.tsv`` Results from pyHMMER search using dbCAN-HMM database. ``overview.tsv`` Consolidated summary of CAZyme predictions across all tools. We recommend focusing on results predicted by at least two tools. CGC (CAZyme Gene Cluster) Annotation ----------------------------------- Next, let's identify and analyze CAZyme gene clusters (CGCs). **Example 1: Prokaryotic Genome with Generated GFF** .. code-block:: shell # Run CGC annotation with automatically generated GFF run_dbcan easy_CGC \ --input_raw_data EscheriaColiK12MG1655.fna \ --mode prok \ --output_dir output_EscheriaColiK12MG1655_fna_CGC \ --db_dir db \ --input_gff gff \ --gff_type prodigal **Example 2: Prokaryotic Proteome with External GFF** .. code-block:: shell # Download example GFF file wget -q https://bcb.unl.edu/dbCAN2/download/test/NCBI_prok_test/EscheriaColiK12MG1655.gff -O EscheriaColiK12MG1655.gff # Run CGC annotation with provided GFF run_dbcan easy_CGC \ --input_raw_data EscheriaColiK12MG1655.faa \ --mode protein \ --output_dir output_EscheriaColiK12MG1655_faa_CGC \ --db_dir db \ --input_gff EscheriaColiK12MG1655.gff \ --gff_type NCBI_prok **Example 3: Eukaryotic Proteome with External GFF** .. code-block:: shell # Download example eukaryotic GFF file wget -q https://bcb.unl.edu/dbCAN2/download/test/NCBI_euk_test/Xylona_heveae_TC161.gff -O Xylona_heveae_TC161.gff # Run CGC annotation run_dbcan easy_CGC \ --input_raw_data Xylona_heveae_TC161.faa \ --mode protein \ --output_dir output_Xylona_heveae_TC161_faa_CGC \ --db_dir db \ --input_gff Xylona_heveae_TC161.gff \ --gff_type NCBI_euk **Example 4: JGI Format Data** .. code-block:: shell # Download JGI format GFF file wget -q https://bcb.unl.edu/dbCAN2/download/test/JGI_test/Xylhe1_GeneCatalog_proteins_20130827.gff -O Xylhe1_GeneCatalog_proteins_20130827.gff # Run CGC annotation run_dbcan easy_CGC \ --input_raw_data Xylhe1_GeneCatalog_proteins_20130827.aa.fasta \ --mode protein \ --output_dir output_Xylhe1_faa_CGC \ --db_dir db \ --input_gff Xylhe1_GeneCatalog_proteins_20130827.gff \ --gff_type JGI CGC Annotation Output Files ----------------------------- In addition to the CAZyme annotation outputs, CGC analysis produces: ``non_CAZyme.faa`` Non-CAZyme protein sequences extracted from uniInput.faa based on overview results. ``diamond.out.tc`` DIAMOND BLAST results against TCDB for transporter protein annotation. ``TF_hmm_results.tsv`` pyHMMER results using TF-HMM database for transcription factor identification. ``STP_hmm_results.tsv`` pyHMMER results using STP-HMM for signal transduction protein identification. ``total_cgc_info.tsv`` Comprehensive annotation of all signature proteins (CAZymes, TC, TF, STP). ``cgc.gff`` Input file for CGCFinder in GFF format, generated from the input GFF and signature annotations. ``cgc_standard_out.tsv`` Standard output from CGCFinder showing identified CAZyme gene clusters. Substrate Prediction ---------------------- Finally, let's predict substrates for the identified CAZymes and CGCs. **Example 1: Prokaryotic Genome** .. code-block:: shell # Run substrate prediction run_dbcan easy_substrate \ --input_raw_data EscheriaColiK12MG1655.fna \ --mode prok \ --output_dir output_EscheriaColiK12MG1655_fna_sub \ --db_dir db \ --input_gff gff \ --gff_type prodigal **Example 2: Prokaryotic Proteome** .. code-block:: shell # Run substrate prediction run_dbcan easy_substrate \ --input_raw_data EscheriaColiK12MG1655.faa \ --mode protein \ --output_dir output_EscheriaColiK12MG1655_faa_sub \ --db_dir db \ --input_gff EscheriaColiK12MG1655.gff \ --gff_type NCBI_prok **Example 3: Eukaryotic Proteome** .. code-block:: shell # Run substrate prediction run_dbcan easy_substrate \ --input_raw_data Xylona_heveae_TC161.faa \ --mode protein \ --output_dir output_Xylona_heveae_TC161_faa_sub \ --db_dir db \ --input_gff Xylona_heveae_TC161.gff \ --gff_type NCBI_euk **Example 4: JGI Format Data** .. code-block:: shell # Run substrate prediction run_dbcan easy_substrate \ --input_raw_data Xylhe1_GeneCatalog_proteins_20130827.aa.fasta \ --mode protein \ --output_dir output_Xylhe1_faa_sub \ --db_dir db \ --input_gff Xylhe1_GeneCatalog_proteins_20130827.gff \ --gff_type JGI Substrate Prediction Output Files ----------------------------------- In addition to previous outputs, substrate prediction produces: ``substrate_prediction.tsv`` Final output containing predicted substrates for each CAZyme gene cluster. ``PUL_blast.out`` DIAMOND blastp results from comparing CGCs against dbCAN-PULs database. ``synteny_pdf/`` Directory containing synteny plots showing gene cluster mappings between PULs and CGCs.