The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

作者: Ross Overbeek , Robert Olson , Gordon D. Pusch , Gary J. Olsen , James J. Davis

DOI: 10.1093/NAR/GKT1226

关键词:

摘要: Abstract In 2004, the SEED (http://pubseed. theseed. org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses …

参考文章(35)
Eugene V. Koonin, Michael Y. Galperin, Genome Annotation and Analysis Kluwer Academic. pp. 193- 226 ,(2003) , 10.1007/978-1-4757-3783-7_6
Scott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A. Best, Christopher Henry, Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED. Methods of Molecular Biology. ,vol. 985, pp. 17- 45 ,(2013) , 10.1007/978-1-62703-299-5_2
Kathi Canese, Sarah Weis, PubMed: The Bibliographic Database National Center for Biotechnology Information (US). ,(2013)
Hal S Alper, Hal S Alper, None, Systems metabolic engineering : methods and protocols Humana Press. ,(2013)
Gordon D. Pusch, Michael Fonstein, Natalia Maltsev, Mark D'Souza, Ross A. Overbeek, Use of contiguity on the chromosome to predict functional coupling. in Silico Biology. ,vol. 1, pp. 93- 108 ,(1999)
C. J. Bult, O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. FitzGerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J.-F. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodek, J. L. Scott, N. S. M. Geoghagen, J. F. Weidman, J. L. Fuhrmann, D. Nguyen, T. R. Utterback, J. M. Kelley, J. D. Peterson, P. W. Sadow, M. C. Hanna, M. D. Cotton, K. M. Roberts, M. A. Hurst, B. P. Kaine, M. Borodovsky, H.-P. Klenk, C. M. Fraser, H. O. Smith, C. R. Woese, J. C. Venter, COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII) Science. ,vol. 273, pp. 1058- 1073 ,(1997) , 10.1126/SCIENCE.273.5278.1058
Robert D Fleischmann, Mark D Adams, Owen White, Rebecca A Clayton, Ewen F Kirkness, Anthony R Kerlavage, Carol J Bult, Jean-Francois Tomb, Brian A Dougherty, Joseph M Merrick, Keith McKenney, Granger Sutton, Will FitzHugh, Chris Fields, Jeannine D Gocayne, John Scott, Robert Shirley, Li-lng Liu, Anna Glodek, Jenny M Kelley, Janice F Weidman, Cheryl A Phillips, Tracy Spriggs, Eva Hedblom, Matthew D Cotton, Teresa R Utterback, Michael C Hanna, David T Nguyen, Deborah M Saudek, Rhonda C Brandon, Leah D Fine, Janice L Fritchman, Joyce L Fuhrmann, NSM Geoghagen, Cheryl L Gnehm, Lisa A McDonald, Keith V Small, Claire M Fraser, Hamilton O Smith, J Craig Venter, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. ,vol. 269, pp. 496- 512 ,(1995) , 10.1126/SCIENCE.7542800
Folker Meyer, Ross Overbeek, Alex Rodriguez, FIGfams: yet another set of protein families Nucleic Acids Research. ,vol. 37, pp. 6643- 6654 ,(2009) , 10.1093/NAR/GKP698
James J. Davis, Gary J. Olsen, Ross Overbeek, Veronika Vonstein, Fangfang Xia, In search of genome annotation consistency: solid gene clusters and how to use them 3 Biotech. ,vol. 4, pp. 331- 335 ,(2014) , 10.1007/S13205-013-0152-2