The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

TitleThe subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Publication TypeJournal Article
Year of Publication2005
AuthorsOverbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V
JournalNucleic Acids Res
Volume33
Issue17
Pagination5691-702
Date Published2005
ISSN1362-4962
KeywordsAcyl Coenzyme A, Coenzyme A, Computational Biology, Genome, Archaeal, Genome, Bacterial, Genomics, Internet, Leucine, Ribosomal Proteins, Software, Terminology as Topic, Vocabulary, Controlled
Abstract

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

DOI10.1093/nar/gki866
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16214803?dopt=Abstract
PMCPMC1251668
Alternate JournalNucleic Acids Res.
PubMed ID16214803