publication . Other literature type . Article . 2008

The RAST Server: Rapid Annotations using Subsystems Technology

Leslie Klis McNeil; Veronika Vonstein; Matthew DeJongh; Kevin Formsma; Elizabeth M. Glass; Gordon D. Pusch; Andrei L. Osterman; Ramy K. Aziz; Ramy K. Aziz; Robert Olson; ...
Open Access
  • Published: 01 Feb 2008
  • Publisher: Springer Science and Business Media LLC
Abstract
<p>Abstract</p> <p>Background</p> <p>The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.</p> <p>Description</p> <p>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 ...
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Database, Biotechnology, TP248.13-248.65, QH426-470, Fully automated, Annotation, DNA microarray, Metabolic network, Genetics, Biology, Pan-genome, Genome project, Genome, Information retrieval, Pathogenomics
28 references, page 1 of 2

Meyer, F, Goesmann, A, McHardy, AC, Bartels, D, Bekel, T, Clausen, J, Kalinowski, J, Linke, B, Rupp, O, Giegerich, R. GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003; 31: 2187-2195 [OpenAIRE] [PubMed] [DOI]

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: W455-459 [OpenAIRE] [PubMed] [DOI]

Bryson, K, Loux, V, Bossy, R, Nicolas, P, Chaillou, S, van de Guchte, M, Penaud, S, Maguin, E, Hoebeke, M, Bessieres, P. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 2006; 34: 3533-3545 [OpenAIRE] [PubMed] [DOI]

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: 53-65 [OpenAIRE] [PubMed] [DOI]

Moriya, Y, Itoh, M, Okuda, S, Yoshizawa, AC, Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007: W182-185 [OpenAIRE] [PubMed] [DOI]

Manatee.

McNeil, LK, Reich, C, Aziz, RK, Bartels, D, Cohoon, M, Disz, T, Edwards, RA, Gerdes, S, Hwang, K, Kubal, M. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007: D347-353 [OpenAIRE] [PubMed] [DOI]

Overbeek, R, Begley, T, Butler, RM, Choudhuri, JV, Chuang, HY, Cohoon, M, de Crecy-Lagard, V, Diaz, N, Disz, T, Edwards, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33: 5691-5702 [OpenAIRE] [PubMed] [DOI]

The SEED framework for comparative genomics.

The Project to Annotate 1000 Genomes.

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: 22-28 [OpenAIRE] [PubMed] [DOI]

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: 1013-1021 [OpenAIRE] [PubMed] [DOI]

Wu, CH, Nikolskaya, A, Huang, H, Yeh, LS, Natale, DA, Vinayaka, CR, Hu, ZZ, Mazumder, R, Kumar, S, Kourtesis, P. PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2004: D112-114 [OpenAIRE] [PubMed] [DOI]

Kanehisa, M, Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28: 27-30 [OpenAIRE] [PubMed] [DOI]

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: 41-43 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
Abstract
<p>Abstract</p> <p>Background</p> <p>The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.</p> <p>Description</p> <p>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 ...
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Database, Biotechnology, TP248.13-248.65, QH426-470, Fully automated, Annotation, DNA microarray, Metabolic network, Genetics, Biology, Pan-genome, Genome project, Genome, Information retrieval, Pathogenomics
28 references, page 1 of 2

Meyer, F, Goesmann, A, McHardy, AC, Bartels, D, Bekel, T, Clausen, J, Kalinowski, J, Linke, B, Rupp, O, Giegerich, R. GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003; 31: 2187-2195 [OpenAIRE] [PubMed] [DOI]

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: W455-459 [OpenAIRE] [PubMed] [DOI]

Bryson, K, Loux, V, Bossy, R, Nicolas, P, Chaillou, S, van de Guchte, M, Penaud, S, Maguin, E, Hoebeke, M, Bessieres, P. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 2006; 34: 3533-3545 [OpenAIRE] [PubMed] [DOI]

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: 53-65 [OpenAIRE] [PubMed] [DOI]

Moriya, Y, Itoh, M, Okuda, S, Yoshizawa, AC, Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007: W182-185 [OpenAIRE] [PubMed] [DOI]

Manatee.

McNeil, LK, Reich, C, Aziz, RK, Bartels, D, Cohoon, M, Disz, T, Edwards, RA, Gerdes, S, Hwang, K, Kubal, M. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007: D347-353 [OpenAIRE] [PubMed] [DOI]

Overbeek, R, Begley, T, Butler, RM, Choudhuri, JV, Chuang, HY, Cohoon, M, de Crecy-Lagard, V, Diaz, N, Disz, T, Edwards, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33: 5691-5702 [OpenAIRE] [PubMed] [DOI]

The SEED framework for comparative genomics.

The Project to Annotate 1000 Genomes.

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: 22-28 [OpenAIRE] [PubMed] [DOI]

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: 1013-1021 [OpenAIRE] [PubMed] [DOI]

Wu, CH, Nikolskaya, A, Huang, H, Yeh, LS, Natale, DA, Vinayaka, CR, Hu, ZZ, Mazumder, R, Kumar, S, Kourtesis, P. PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2004: D112-114 [OpenAIRE] [PubMed] [DOI]

Kanehisa, M, Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28: 27-30 [OpenAIRE] [PubMed] [DOI]

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: 41-43 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
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