Summary
Grasses are one of the largest agricultural crops, providing food, industrial materials and renewable energy sources. Due to their large genome size and the number of the species in the taxa, many of the genomes are not targeted for complete sequencing. Gramene seeks to provide basic researchers, industry and educators with a resource that can be used as a tool for knowledge discovery across grass species. This chapter briefly outlines system requirements for end users and database hosting, outlines data types and basic navigation within Gramene and provides an example of how a maize researcher would use Gramene to leverage rice genome organization and phenotypic information to support targeted experimental research in maize.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Reference
Jaiswal, P., Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T.M., Buckler, E.S., Stein, L., and McCouch S. (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res. 34, D717–D723.
Ware, D., Jaiswal, P., Ni, J., Pan, X., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., et al. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 30 (1), 103–105.
Birney, E., Andrews, T. D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X. M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H.R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K. C., Cameron, G., Durbin, R., Cox, A., Hubbard, T., and Clamp, M. (2004) An overview of Ensembl. Genome Res. 14, 925–928.
Lomax, J. (2005) Get ready to GO! A biologist’s guide to the Gene Ontology. Brief. Bioinform. 6, 298–304.
Clark, J.I., Brooksbank, C. and Lomax, J. (2005) It’s all GO for plant scientists. Plant Physiol. 138, 1268–1278.
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones. S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L.L., Studholme, D.J., Yeats, C., Eddy, S.R. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138–D141.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. (2006) Genbank. Nucleic Acids Res. 34, 16–20.
Lawrence, C.J., Dong, Q., Polacco, M.L., Seigfried, T.E., and Brendel, V. (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res. 32, D393–D397.
Matthews, D.E., Carollo, V.L., Lazo, G.R., and Anderson, O.D. (2003) GrainGenes, the genome database for small-grain crops. Nucleic Acids Res. 31, 183–186.
Carollo, V., Matthews, D.E., Lazo, G.R., Blake, T.K., Hummel, D.D., Lui, N., Hane, D.L., and Anderson, O.D. (2005) GrainGenes 2.0. An improved resource for the small-grains community. Plant Physiol. 139, 643–651.
Shen, L., Gong, J., Caldo, R.A., Nettleton, D., Cook, D., Wise, R.P., and Dickerson, J.A. (2005) BarleyBase–an expression profiling database for plant genomics. Nucleic Acids Res. 33 (1), D614–D618.
Du, C.G., Buckler, E., and Muse, S. (2003) Development of a maize molecular evolutionary genomic database. Comp Funct Genomics 4 (2), 246–249.
Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L., and Ware, D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res. 34 (1), D752.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Ware, D. (2007). Gramene. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology™, vol 406. Humana Press. https://doi.org/10.1007/978-1-59745-535-0_15
Download citation
DOI: https://doi.org/10.1007/978-1-59745-535-0_15
Publisher Name: Humana Press
Print ISBN: 978-1-58829-653-5
Online ISBN: 978-1-59745-535-0
eBook Packages: Springer Protocols