Journal
BIOINFORMATICS
Volume 31, Issue 5, Pages 647-655Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu716
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Funding
- European Research Council under European Union's Seventh Framework Program (FP)/ERC Grant [322820]
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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.
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