Quantitative assessment of protein function prediction from metagenomics shotgun sequences.

ABSTRACT: To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associat

SUBMITTER: Harrington ED 

PROVIDER: S-EPMC1955820 | biostudies-literature | 2007 Aug

REPOSITORIES: biostudies-literature