Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

作者：Terrapon Nicolas^*; Lombard Vincent; Gilbert Harry J; Henrissat Bernard

来源：Bioinformatics, 2015, 31(5): 647-655.

DOI：10.1093/bioinformatics/btu716

Motivation: A bacterial polysaccharide utilization locus (PUL) is a set of physically linked genes that orchestrate the breakdown of a specific glycan. PULs are prevalent in the Bacteroidetes phylum and are key to the digestion of complex carbohydrates, notably by the human gut microbiota. A given Bacteroidetes genome can encode dozens of different PULs whose boundaries and precise gene content are difficult to predict.
Results: Here, we present a fully automated approach for PUL prediction using genomic context and domain annotation alone. By combining the detection of a pair of marker genes with operon prediction using intergenic distances, and queries to the carbohydrate-active enzymes database (www.cazy.org), our predictor achieved above 86% accuracy in two Bacteroides species with extensive experimental PUL characterization.

• 出版日期2015-3-1