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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
Open accessAbstract
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 subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
High-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, C. S., DeJongh, M., Best, A. A., Frybarger, P. M., Linsay, B., & Stevens, R. L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1672 · Cited by 1,090
Self-citation
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Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709
Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., & Tappu, R. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004957 · Cited by 1,761
Probiotics, gut microbiota, and their influence on host health and disease
Sánchez, B., Delgado, S., Blanco‐Míguez, A., Lourenço, A., Gueimonde, M., & Margolles, A. (2017) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600240 · Cited by 1,104
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V., & Thiele, I. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00148 · Cited by 876
Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M. J., Trehan, I., Jorgensen, J. M., et al. (2016) · Science · doi:10.1126/science.aad3311 · Cited by 735
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Li, H., Limenitakis, J. P., Fuhrer, T., Geuking, M. B., Lawson, M. A., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J. A., Rupp, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9292 · Cited by 511
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Langille, M. G., Meehan, C. J., Koenig, J. E., Dhanani, A. S., Rose, R. A., Howlett, S. E., & Beiko, R. G. (2014) · Microbiome · doi:10.1186/s40168-014-0050-9 · Cited by 437
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Gehrig, J. L., Venkatesh, S., Chang, H.-W., Hibberd, M. C., Kung, V. L., Cheng, J., Chen, R. Y., Subramanian, S., Cowardin, C. A., Meier, M. F., et al. (2019) · Science · doi:10.1126/science.aau4732 · Cited by 431
Williams, M. R., Costa, S. K., Zaramela, L. S., Khalil, S., Todd, D. A., Winter, H. L., Sanford, J. A., O’Neill, A. M., Liggins, M. C., Nakatsuji, T., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aat8329 · Cited by 292
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“The RAST annotation pipeline (Overbeek et al., 2014) suggests the putative ROK family gene 0495 codes for N-acetylmannosamine kinase (NagC).”
BackgroundMethodMoretti, S., Martin, O., Van Du Tran, T., Bridge, A., Morgat, A., & Pagni, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1117 · Cited by 162
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Schmid, M., Frei, D., Patrignani, A., Schlapbach, R., Frey, J. E., Remus-Emsermann, M. N. P., & Ahrens, C. H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky726 · Cited by 92
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Roalkvam, I., Drønen, K., Stokke, R., Daae, F. L., Dahle, H., & Steen, I. H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00987 · Cited by 77
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Surve, S., Shinde, D. B., & Kulkarni, R. (2022) · Scientific Reports · doi:10.1038/s41598-022-05850-3 · Cited by 74
Pataky, Z., Genton, L., Spahr, L., Lazarevic, V., Terraz, S., Gaïa, N., Rubbia-Brandt, L., Golay, A., Schrenzel, J., & Pichard, C. (2016) · Digestive Diseases and Sciences · doi:10.1007/s10620-016-4179-1 · Cited by 75
Dmitrijeva, M., Tackmann, J., Matias Rodrigues, J. F., Huerta-Cepas, J., Coelho, L. P., & von Mering, C. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02357-0 · Cited by 72
Somashekaraiah, R., Mottawea, W., Gunduraj, A., Joshi, U., Hammami, R., & Sreenivasa, M. Y. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.696267 · Cited by 66
Knippel, R. J., Wexler, A. G., Miller, J. M., Beavers, W. N., Weiss, A., de Crécy-Lagard, V., Edmonds, K. A., Giedroc, D. P., & Skaar, E. P. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.05.015 · Cited by 62
Panas, M. W., Jain, P., Yang, H., Mitra, S., Biswas, D., Wattam, A. R., Letvin, N. L., & Jacobs, W. R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414207111 · Cited by 62
Self-citationForde, T. L., Orsel, K., Zadoks, R. N., Biek, R., Adams, L. G., Checkley, S. L., Davison, T., De Buck, J., Dumond, M., Elkin, B. T., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01759 · Cited by 50
Castro-Severyn, J., Pardo-Esté, C., Mendez, K. N., Fortt, J., Marquez, S., Molina, F., Castro-Nallar, E., Remonsellez, F., & Saavedra, C. P. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00444-21 · Cited by 36
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Prah, I., Ayibieke, A., Mahazu, S., Sassa, C. T., Hayashi, T., Yamaoka, S., Suzuki, T., Iwanaga, S., Ablordey, A., & Saito, R. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1920342 · Cited by 27
Scaria, J., Suzuki, H., Ptak, C. P., Chen, J.-W., Zhu, Y., Guo, X.-K., & Chang, Y.-F. (2015) · BMC Genomics · doi:10.1186/s12864-015-1663-5 · Cited by 26
Suenaga, H., Fujihara, H., Kimura, N., Hirose, J., Watanabe, T., Futagami, T., Goto, M., Shimodaira, J., & Furukawa, K. (2017) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12561 · Cited by 26
Klanchui, A., Dulsawat, S., Chaloemngam, K., Cheevadhanarak, S., Prommeenate, P., & Meechai, A. (2018) · Metabolites · doi:10.3390/metabo8040084 · Cited by 24
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Xie, Z., Wang, D., Ben Fekih, I., Yu, Y., Li, Y., Alwathnani, H., Herzberg, M., & Rensing, C. (2023) · Microorganisms · doi:10.3390/microorganisms11061518 · Cited by 11
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Fatima, S., Butt, H. A., Aftab, A., & Bakhtiar, S. M. (2021) · Pakistan Journal of Biochemistry and Biotechnology · doi:10.52700/pjbb.v2i2.46 · Cited by 1
Metadata
- Authors
- Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F., & Stevens, R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-29
- Volume
- 42
- Issue
- D1
- Pages
- D206-D214
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2142428670
- Cited by
- 4,524
- References
- 2
- FWCI
- 90.37
- Type
- journal article
- Language
- en
- Open access
- gold
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