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

Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, de Crecy-Lagard, Valerie, Diaz, Naryttza, Disz, Terry, Edwards, Robert, Fonstein, Michael, Frank, Ed D., Gerdes, Svetlana, Glass, Elizabeth M., Goesmann, Alexander, Hanson, Andrew, Iwata-Reuyl, Dirk, Jensen, Roy, Jamshidi, Neema, Krause, Lutz, Kubal, Michael, Larsen, Niels, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Neuweger, Heiko, Olsen, Gary, Olson, Robert, Osterman, Andrei, Portnoy, Vasiliy, Pusch, Gordon D., Rodionov, Dmitry A., Ruckert, Christian, Steiner, Jason, Stevens, Rick, Thiele, Ines, Vassieva, Olga, Ye, Yuzhen, Zagnitko, Olga and Vonstein, Veronika (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33 17: 5691-5702. doi:10.1093/nar/gki866

Author Overbeek, Ross
Begley, Tadhg
Butler, Ralph M.
Choudhuri, Jomuna V.
Chuang, Han-Yu
Cohoon, Matthew
de Crecy-Lagard, Valerie
Diaz, Naryttza
Disz, Terry
Edwards, Robert
Fonstein, Michael
Frank, Ed D.
Gerdes, Svetlana
Glass, Elizabeth M.
Goesmann, Alexander
Hanson, Andrew
Iwata-Reuyl, Dirk
Jensen, Roy
Jamshidi, Neema
Krause, Lutz
Kubal, Michael
Larsen, Niels
Linke, Burkhard
McHardy, Alice C.
Meyer, Folker
Neuweger, Heiko
Olsen, Gary
Olson, Robert
Osterman, Andrei
Portnoy, Vasiliy
Pusch, Gordon D.
Rodionov, Dmitry A.
Ruckert, Christian
Steiner, Jason
Stevens, Rick
Thiele, Ines
Vassieva, Olga
Ye, Yuzhen
Zagnitko, Olga
Vonstein, Veronika
Title The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2005-01-01
Year available 2005
Sub-type Article (original research)
DOI 10.1093/nar/gki866
Open Access Status DOI
Volume 33
Issue 17
Start page 5691
End page 5702
Total pages 12
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted 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.
Keyword Biochemistry & Molecular Biology
Biochemistry & Molecular Biology
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
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