The biofuel feedstock genomics resource: A web-based portal and database to enable functional genomics of plant biofuel feedstock species

Database

Volumn 2012, Issue , 2012, Pages

  Childs, Kevin L ^a   Konganti, Kranti ^a   Buell, C Robin ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PANICUM VIRGATUM; POPULUS; ZEA MAYS;

BIOFUEL; TRANSCRIPTOME;

ARTICLE; BIOMASS; DATA BASE; GENETIC DATABASE; GENOMICS; INTERNET; PLANT GENOME;

BIOFUELS; BIOMASS; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENOME, PLANT; GENOMICS; INTERNET; TRANSCRIPTOME;

EID: 84864041933     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bar061     Document Type: Article

References (36)

1. Tyner, W.E. (2010) The integration of energy and agricultural markets. Agric. Econ., 41, 193-201.
2. Mueller, S.A., Anderson, J.E. and Wallington, T.J. (2011) Impact of biofuel production and other supply and demand factors on food price increases in 2008. Biomass Bioenergy, 35, 1623-1632.
3. Banerjee, A. (2011) Food, feed, fuel: Transforming the competition for grains. Dev. Change, 42, 529-557.
4. Hinchee, M., Rottmann, W., Mullinax, L. et al. (2009) Short-rotation woody crops for bioenergy and biofuels applications. In Vitro Cell Dev. Biol. Plant, 45, 619-629.
5. Kline, K.L. and Coleman, M.D. (2010) Woody energy crops in the southeastern United States: Two centuries of practitioner experience. Biomass Bioenergy, 34, 1655-1666.
6. Naik, S., Goud, V.V., Rout, P.K. et al. (2010) Characterization of Canadian biomass for alternative renewable biofuel. Renew. Energy, 35, 1624-1631.
7. Somerville, C., Youngs, H., Taylor, C. et al. (2010) Feedstocks for lignocellulosic biofuels. Science, 329, 790-792.
8. Wroblewska, H., Komorowicz, M., Pawlowski, J. et al. (2009) Chemical and energetical properites of selected lignocellulosic raw materials. Folia Forestalia Polonica, 40, 67-78.
9. Sanderson, M.A. and Adler, P.R. (2008) Perennial forages as second generation bioenergy crops. Int. J. Mol. Sci., 9, 768-88. (Pubitemid 351776195)
10. Lawrence, C.J., Harper, L.C., Schaeffer, M.L. et al. (2008) MaizeGDB: The maize model organism database for basic, translational, and applied research. Int. J. Plant Genomics, 2008, 496957.
11. Liang, C., Jaiswal, P., Hebbard, C. et al. (2008) Gramene: A growing plant comparative genomics resource. Nucleic Acids Res., 36, D947-D953. (Pubitemid 351149850)
12. Tuskan, G.A., Difazio, S., Jansson, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596-1604. (Pubitemid 44414027)
13. Paterson, A.H., Bowers, J.E., Bruggmann, R. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551-556.
14. Schnable, P.S., Ware, D., Fulton, R.S. et al. (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science, 326, 1112-11125.
15. Duvick, J., Fu, A., Muppirala, U. et al. (2008) PlantGDB: A resource for comparative plant genomics. Nucleic Acids Res., 36, D959-D965. (Pubitemid 351149852)
16. Childs, K.L., Hamilton, J.P., Zhu, W. et al. (2007) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res., 35, D846-D851. (Pubitemid 46056320)
17. Sayers, E.W., Barrett, T., Benson, D.A. et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.
18. Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
19. Gish, W. and States, D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet., 3, 266-272. (Pubitemid 23096565)
20. The UniProt Consortium. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
21. Mulder, N.J., Apweiler, R., Attwood, T.K. et al. (2007) New developments in the InterPro database. Nucleic Acids Res., 35, D224-D228. (Pubitemid 46056203)
22. Kanehisa, M., Araki, M., Goto, S. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484. (Pubitemid 351149770)
23. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
24. International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763-768.
25. Jaillon, O., Aury, J.M., Noel, B. et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463-467. (Pubitemid 47509545)
26. The International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
27. Iseli, C., Jongeneel, C.V. and Bucher, P. (1999) ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 138-148.
28. Camon, E., Magrane, M., Barrell, D. et al. (2004) The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res., 32, D262-D266. (Pubitemid 38081652)
29. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
30. Li, L., Stoeckert, C.J. Jr and Roos, D.S. (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189. (Pubitemid 37161775)
31. Edgar, R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797. (Pubitemid 38832724)
32. Zhou, P., Emmert, D. and Zhang, P. (2006) Using Chado to store genome annotation data. Curr. Protoc. Bioinformatics, Chapter 9, Unit 9 6.
33. Mungall, C.J. and Emmert, D.B. (2007) A Chado case study: An ontology-based modular schema for representing genomeassociated biological information. Bioinformatics, 23, i337-i346. (Pubitemid 47244418)
34. Stein, L.D., Mungall, C., Shu, S. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610. (Pubitemid 35175099)
35. Huang, X. (1994) On global sequence alignment. Comput. Appl. Biosci., 10, 227-235. (Pubitemid 24197987)
36. Hahlbrock, K. and Scheel, D. (1989) Physiology and molecular biology of phenylpropanoid metabolism. Annu. Rev. Plant Physiol. Plant Mol. Biol., 40, 347-369.