A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

ABSTRACT: A common biological pathway reconstruction approach -- as implemented by many automatic biological pathway services (such as the KAAS and RAST servers) and the functional annotation of metagenomic sequences -- starts with the identification of protein functions or families (e.g., KO families for the KEGG database and the FIG families for the SEED database) in the query sequences, followed by a direct mapping of the identified protein families onto pathways. Given a predicted patchwork of individual biochemical steps, some metric must be applied in deciding what pathways actually exist in the genome or metagenome represented by the sequences. Commonly, and straightforwardly, a complete biological pathway can be identified in a dataset if at least one of the steps associated with the pathway

SUBMITTER: Ye Y 

PROVIDER: S-EPMC2714467 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature