Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

ABSTRACT: Environmental shotgun sequencing (or metagenomics) is widely used to survey the communities of microbial organisms that live in many diverse ecosystems, such as the human body. Finding the protein-coding genes within the sequences is an important step for assessing the functional capacity of a metagenome. In this work, we developed a metagenomics gene prediction system Glimmer-MG that achieves significantly greater accuracy than previous systems via novel approaches to a number of important prediction subtasks. First, we introduce the use of phylogenetic classifications of the sequences to model parameterization. We also cluster the sequences, grouping together those that likely originated from the same organism. Analogous to iterative schemes that are useful for whole genomes, we retrain

SUBMITTER: Kelley DR 

PROVIDER: S-EPMC3245904 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature