The RAST Server: Rapid Annotations using Subsystems Technology

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• 作者：Ramy K Aziz (8) (9)
  Daniela Bartels (3)
  Aaron A Best (7)
  Matthew DeJongh (7)
  Terrence Disz (2) (3)
  Robert A Edwards (1) (2)
  Kevin Formsma (7)
  Svetlana Gerdes (1)
  Elizabeth M Glass (2)
  Michael Kubal (3)
  Folker Meyer (2) (3)
  Gary J Olsen (2) (4)
  Robert Olson (2) (3)
  Andrei L Osterman (1) (5)
  Ross A Overbeek (1)
  Leslie K McNeil (6)
  Daniel Paarmann (3)
  Tobias Paczian (3)
  Bruce Parrello (1)
  Gordon D Pusch (1) (3)
  Claudia Reich (6)
  Rick Stevens (2) (3)
  Olga Vassieva (1)
  Veronika Vonstein (1)
  Andreas Wilke (3)
  Olga Zagnitko (1)
  
• 刊名：BMC Genomics
• 出版年：2008
• 出版时间：December 2008
• 年：2008
• 卷：9
• 期：1
• 全文大小：3474KB
• 参考文献：1. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, / et al.: GenDB - an open source genome annotation system for prokaryote genomes. / Nucleic Acids Res 2003,31(8):2187-195. CrossRef
  2. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS: BASys: a web server for automated bacterial genome annotation. / Nucleic Acids Res 2005, (33 Web Server):W455-59.
  3. Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessieres P, / et al.: AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. / Nucleic Acids Res 2006,34(12):3533-545. CrossRef
  4. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Medigue C: MaGe: a microbial genome annotation system supported by synteny results. / Nucleic Acids Res 2006,34(1):53-5. CrossRef
  5. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M: KAAS: an automatic genome annotation and pathway reconstruction server. / Nucleic Acids Res 2007, (35 Web Server):W182-85.
  6. Manatee[http://manatee.sourceforge.net]
  7. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, / et al.: The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. / Nucleic Acids Res 2007, (35 Database):D347-53.
  8. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, / et al.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. / Nucleic Acids Res 2005,33(17):5691-702. CrossRef
  9. The SEED framework for comparative genomics[http://www.theseed.org]
  10. The Project to Annotate 1000 Genomes[http://www.theSEED.org/wiki/Annotating_1000_genomes]
  11. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. / Nucleic Acids Res 2001,29(1):22-8. CrossRef
  12. Schneider M, Tognolli M, Bairoch A: The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. / Plant Physiol Biochem 2004,42(12):1013-021. CrossRef
  13. Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, / et al.: PIRSF: family classification system at the Protein Information Resource. / Nucleic Acids Res 2004, (32 Database):D112-14.
  14. Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. / Nucleic Acids Res 2000,28(1):27-0. CrossRef
  15. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O: TIGRFAMs: a protein family resource for the functional identification of proteins. / Nucleic Acids Res 2001,29(1):41-3. CrossRef
  16. Overbeek R, Bartels D, Vonstein V, Meyer F: Annotation of bacterial and archaeal genomes: improving accuracy and consistency. / Chem Rev 2007,107(8):3431-447. CrossRef
  17. Wu CH, Shivakumar S: Proclass protein family database: new version with motif alignments. / Pac Symp Biocomput 1998, 719-30.
  18. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. / Nucleic Acids Res 1997,25(5):955-64. CrossRef
  19. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. / Nucleic Acids Res 1999,27(23):4636-641. CrossRef
  20. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A: Toward the automated generation of genome-scale metabolic networks in the SEED. / BMC Bioinformatics 2007, 8:139. CrossRef
  21. Becker SA, Palsson BO: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. / BMC Microbiol 2005,5(1):8. CrossRef
  22. KAAS - KEGG Automatic Annotation Server[http://www.genome.jp/kegg/kaas/]
  23. The Annotation Clearinghouse[http://clearinghouse.nmpdr.org]
  24. TIGR's Comprehensive Microbial Resource[http://cmr.tigr.org]
  25. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. / Nucleic Acids Res 2007, (35 Database):D21-5.
  26. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, / et al.: The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. / Nucleic Acids Res 2008, (36 Database):D528-33.
  27. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, / et al.: KEGG for linking genomes to life and the environment. / Nucleic Acids Res 2008, (36 Database):D480-84.
  28. The metagenomics RAST server[http://metagenomics.nmpdr.org]
  
• 作者单位：Ramy K Aziz (8) (9)
  Daniela Bartels (3)
  Aaron A Best (7)
  Matthew DeJongh (7)
  Terrence Disz (2) (3)
  Robert A Edwards (1) (2)
  Kevin Formsma (7)
  Svetlana Gerdes (1)
  Elizabeth M Glass (2)
  Michael Kubal (3)
  Folker Meyer (2) (3)
  Gary J Olsen (2) (4)
  Robert Olson (2) (3)
  Andrei L Osterman (1) (5)
  Ross A Overbeek (1)
  Leslie K McNeil (6)
  Daniel Paarmann (3)
  Tobias Paczian (3)
  Bruce Parrello (1)
  Gordon D Pusch (1) (3)
  Claudia Reich (6)
  Rick Stevens (2) (3)
  Olga Vassieva (1)
  Veronika Vonstein (1)
  Andreas Wilke (3)
  Olga Zagnitko (1)
  
  8. University of Tennessee, Health Science Center, Memphis, TN, 38136, USA
  9. Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
  3. Computation Institute, University of Chicago, Chicago, IL, 60637, USA
  7. Hope College, MI, 49423, USA
  2. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
  1. Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA
  4. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  5. The Burnham Institute, San Diego, CA, 92037, USA
  6. National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  

文摘

Background The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-4 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. Conclusion By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.