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CAZyme Annotation

CAZyme Annotation

Methods: Carbohydrate-Active enZYmes (CAZymes) were observed directly using alignment at 97% identity against a gene database derived from the Diversigen Venti strain database. The CAZyme alignment database was constructed by annotating all genes from all Venti strains for CAZyme content using Hidden Markov Models. Genes that scored better than confidence thresholds were included in the final CAZyme database. Reads were then mapped to said database using the BURST aligner. The absolute counts table was created by counting the number of reads that map to a gene and assigning this count to the CAZyme family/subfamily annotation(s) for that gene. The normalized scores table takes the number of reads that map to a gene, divides by the gene length, and then assigns this length-normalized count value to the CAZyme family/subfamily annotation(s) for that gene. Rigorous testing of the CAZyme database using samples with known CAZyme abundances indicates that the length-normalized table gives a more accurate picture of the true CAZyme profile of a sample.