RiceGeneThresher: A web-based application for mining genes underlying QTL in rice genome

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Thongjuea, Supat ^a,b   Ruanjaichon, Vinitchan ^a   Bruskiewich, Richard ^c   Vanavichit, Apichart ^a  

^a KASETSART UNIVERSITY   (Thailand)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^c INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER;

ARTICLE; DATA BASE; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENE LOCUS; GENETIC MARKER; GENOME; METABOLISM; ONLINE SYSTEM; PLANT STRESS; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; QUANTITATIVE TRAIT LOCUS; RICE; RICEGENE THRESHER; VALIDATION PROCESS;

DATABASES, GENETIC; GENES, PLANT; GENOME, PLANT; GENOMICS; INTERNET; ORYZA SATIVA; QUANTITATIVE TRAIT LOCI; USER-COMPUTER INTERFACE;

EID: 58149182718     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn638     Document Type: Article

References (18)

1. Korstanje,R. and Paigen,B. (2002) From QTL to gene: The harvest begins. Nat. Genet., 31, 235-236.
2. Pflieger,S., Lefebvre,V. and Causse,M. (2001) The candidate gene approach in plant genetics: A review. Mol. Breeding, 7, 275-291.
3. Borevitz,J.O. and Chory,J. (2004) Genomics tools for QTL analysis and gene discovery. Curr. Opin. Plant. Biol., 7, 132-136.
4. Liang,C., Jaiswal,P., Hebbard,C., Avraham,S., Buckler,E.S., Casstevens,T., Hurwitz,B., McCouch,S., Ni,J., Pujar,A. et al. (2008) Gramene: A growing plant comparative genomics resource. Nucleic Acids Res., 36, D947-D953.
5. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
6. Schuler,G.D. (1997) Sequence mapping by electronic PCR. Genome Res. 7, 541-550.
7. Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Binns,D., Bradley,P., Bork,P., Bucher,P., Cerutti,L. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33 D201-D205.
8. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
9. Garcia-Hernandez,M., Berardini,T.Z., Chen,G., Crist,D., Doyle,A., Huala,E., Knee,E., Lambrecht,M., Miller,N., Mueller,L.A. et al. (2002) TAIR: A resource for integrated Arabidopsis data. Funct. Integr. Genomics, 2, 239-253.
10. Yu,H., Luscombe,N.M., Lu,H.X., Zhu,X., Xia,Y., Han,J.-D.J., Bertin,N., Chung,S., Vidal,M. and Gerstein,M. (2004) Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res., 14, 1107-1118.
11. Zmasek,C. and Eddy,S. (2002) RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3, 14.
12. Wanchana,S., Thongjuea,S., Ulat,V.J., Anacleto,M., Mauleon,R., Conte,M., Rouard,M., Ruiz,M., Krishnamurthy,N., Sjolander,K. et al. (2008) The generation challenge programme comparative plant stress-responsive gene catalogue. Nucleic Acids Res., 36, D943-D946.
13. Mungall,C.J. and Emmert,D.B. (2007) A Chado case study: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
14. Wilkinson,M., Schoof,H., Ernst,R. and Haase,D. (2005) BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case. Plant Physiol., 138, 5-17.
15. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
16. Zmasek,C.M. and Eddy,S.R. (2001) ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics, 17, 383-384.
17. Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.
18. Labarga,A., Valentin,F., Anderson,M. and Lopez,R. (2007) Web services at the European Bioinformatics Institute. Nucleic Acids Res., 35 W6-W11.