High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

ABSTRACT: The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its pare

SUBMITTER: Seaver SM 

PROVIDER: S-EPMC4084441 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature