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The TIGR Rice Genome Annotation Resource: improvements and new features

S. Ouyang, W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R. L. Malek, Y. Lee, L. Zheng, J. Orvis, B. Haas (+2 others)
2007 Nucleic Acids Research  
In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation  ...  in the rice genome.  ...  ACKNOWLEDGEMENTS The efforts of the TIGR Bioinformatics department in generating a suite of tools and resources for eukaryotic sequence and annotation are appreciated.  ... 
doi:10.1093/nar/gkl976 pmid:17145706 pmcid:PMC1751532 fatcat:zpp73bez4jcz3og4opisq6bw2q

Gramene: a growing plant comparative genomics resource

C. Liang, P. Jaiswal, C. Hebbard, S. Avraham, E. S. Buckler, T. Casstevens, B. Hurwitz, S. McCouch, J. Ni, A. Pujar, D. Ravenscroft, L. Ren (+9 others)
2007 Nucleic Acids Research  
Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale  ...  Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species.  ...  Oard, David Marshall, Patricia Klein and John Mullet for their critical comments, suggestions and improvements of our work. We also thank Peter Van Buren for his excellent system administration work.  ... 
doi:10.1093/nar/gkm968 pmid:17984077 pmcid:PMC2238951 fatcat:7gqtpirinfc37g44tiynfwftlm

Global Information Resources on Rice for Research and Development

Shri RAM, N. LAXMAN RAO
2012 Rice Science  
The establishment like International Rice Information System, Rice Genome Research Project and Integrated Rice Genome Explorer are major initiatives for the improvement of rice.  ...  This paper will also highlight some of the initiatives and organizations working in the field of rice improvement and explore the availability of the various web resources for the purpose of research and  ...  The Institute for Genomic Research (TIGR) Rice Genome Annotation Project (http://rice.tigr.org) is working in the area of rice genome sequence with new data to improve the quality of the annotation.  ... 
doi:10.1016/s1672-6308(12)60058-4 fatcat:jsbzm66ckzcc7hwf2xeblbfj3u

Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA

M. Nakano
2006 Nucleic Acids Research  
We have created a series of databases for four species 15 (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus).  ...  Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative 20 splice isoforms  ...  These resources include two plant genomes, Arabidopsis and rice, as well as a number of plant pathogen genomes (1) (2) (3) (4) .  ... 
doi:10.1093/nar/gkj077 pmid:16381968 pmcid:PMC1347440 fatcat:rg4bilo6ijex7jwz2toihiuq4m

Comparative Plant Genomics Resources at PlantGDB

Q. Dong
2005 Plant Physiology  
For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete  ...  Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice,  ...  ACKNOWLEDGMENTS We thank Ann Fu and Mike Brekke for their technical contributions to this work.  ... 
doi:10.1104/pp.104.059212 pmid:16219921 pmcid:PMC1255980 fatcat:hzrlccaakvc5nd4dsvah4fafqe

PlantGDB: a resource for comparative plant genomics

J. Duvick, A. Fu, U. Muppirala, M. Sabharwal, M. D. Wilkerson, C. J. Lawrence, C. Lushbough, V. Brendel
2007 Nucleic Acids Research  
Brekke for system support, and the many PlantGDB users who have helped us to improve this resource by providing feedback and suggestions.  ...  and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies.  ...  Key features include: expanded EST assemblies; new genome browsers for a larger number of species; overnight annotation of emerging genome sequences; and novel tools for sequence retrieval and analysis  ... 
doi:10.1093/nar/gkm1041 pmid:18063570 pmcid:PMC2238959 fatcat:g32waehmrnc2xk2e4cvidehgia

Oryzabase: an integrated information resource for rice science

Yukiko Yamazaki, Shingo Sakaniwa, Rie Tsuchiya, Ken-Ichi Nonomura, Nori Kurata
2010 Breeding Science  
The database also contains genetic and genomic maps, and 20,000 items from the published literature.  ...  Of these items, the most valuable are the biological resources, particularly the wild rice and mutant collections, because they have been thoroughly characterized by researchers and are accompanied by  ...  We intend to improve the database to make it more reliable by means of an efficient combination of automatic annotation, manual annotation, and community annotation.  ... 
doi:10.1270/jsbbs.60.544 fatcat:aaxe2wuw7fcl7e24myaabdgwmq

MIPS Arabidopsisthaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

H. Schoof
2002 Nucleic Acids Research  
Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence.  ...  Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published.  ...  Haas and O. White (TIGR), A. Kozik and R. Michelmore (UC Davis), S. Shiu and A. Bleecker (University of Wisconsin), F. Fana and M.  ... 
doi:10.1093/nar/30.1.91 pmid:11752263 pmcid:PMC99069 fatcat:uquftvhr6ngybga7fqw2qr4ut4

MIPSPlantsDB--plant database resource for integrative and comparative plant genome research

M. Spannagl, O. Noubibou, D. Haase, L. Yang, H. Gundlach, T. Hindemitt, K. Klee, G. Haberer, H. Schoof, K. F. X. Mayer
2007 Nucleic Acids Research  
PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato.  ...  The increase in available plant genomic data enables powerful comparative analysis and integrative approaches.  ...  ACKNOWLEDGEMENTS The work has been supported within the GABI project of the German Ministry of Science and Education as well as by funding by the European Commission (framework 6) within the Grain Legumes  ... 
doi:10.1093/nar/gkl945 pmid:17202173 pmcid:PMC1899105 fatcat:nyhl673xwbf6ljlg2qzsdnc6k4

The Arabidopsis Information Resource (TAIR): gene structure and function annotation

D. Swarbreck, C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, A. Radenbaugh, S. Singh (+4 others)
2007 Nucleic Acids Research  
use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007.  ...  New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to  ...  Funding to pay the Open Access publication charges for this article was provided by grant DBI-0417062 from the National Science Foundation.  ... 
doi:10.1093/nar/gkm965 pmid:17986450 pmcid:PMC2238962 fatcat:rxj2mg33bnh25lrcdvmnrtgdzy

PlantTribes: a gene and gene family resource for comparative genomics in plants

P. K. Wall, J. Leebens-Mack, K. F. Muller, D. Field, N. S. Altman, C. W. dePamphilis
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank our faculty, postdoctoral and student colleagues in the Floral Genome Project, the Ancestral Angiosperm Genome Project and the poplar and papaya genome projects for their  ...  enthusiastic support and use of PlantTribes through its initial stages of development.  ...  New features being developed presently include (i) a tool for the rapid incorporation of new query sequences into tribe alignments and phylogenies, (ii) connecting the rapidly expanding microRNA database  ... 
doi:10.1093/nar/gkm972 pmid:18073194 pmcid:PMC2238917 fatcat:4t5jwz2dcfbqrh5hudrkakelce

Genome Sequencing and Genome Resources in Model Legumes

S. Sato, Y. Nakamura, E. Asamizu, S. Isobe, S. Tabata
2007 Plant Physiology  
Giles Oldroyd and Nevin Young for updated information on the M. truncatula genome sequencing project. Received February 3, 2007; accepted March 10, 2007; published June 6, 2007.  ...  A remarkable exception is sequencing of the soybean genome (http://www.energy.gov/news/2979.htm).  ...  The International Medicago Genome Annotation Group has selected a canonical genome annotation procedure.  ... 
doi:10.1104/pp.107.097493 pmid:17556522 pmcid:PMC1914170 fatcat:3ncpdwdlufc5xm77ivxyhieuzu

Genomic resources in plant breeding for sustainable agriculture

Mahendar Thudi, Ramesh Palakurthi, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Odeny, Vijay K. Tiwari, Hon-Ming Lam, Yan Bin Hong (+11 others)
2020 Journal of plant physiology  
In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic  ...  In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants  ...  features and the updated gene models annotation.  ... 
doi:10.1016/j.jplph.2020.153351 pmid:33412425 pmcid:PMC7903322 fatcat:xujybmnnbrdnfnueet55wsb25i

Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses

H. Schoof
2005 Plant Physiology  
, and rice (Oryza sativa).  ...  This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.  ...  We thank all members of the BioMOBY community, the IMGAG, and the PlaNet project for cooperation and helpful discussions on data exchange and standards.  ... 
doi:10.1104/pp.104.059188 pmid:16010004 pmcid:PMC1176403 fatcat:hcuqixozpvha7chxblc5re2xuu

TAIR: a resource for integrated Arabidopsis data

Margarita Garcia-Hernandez, Tanya Berardini, Guanghong Chen, Debbie Crist, Aisling Doyle, Eva Huala, Emma Knee, Mark Lambrecht, Neil Miller, Lukas Mueller, Suparna Mundodi, Leonore Reiser (+9 others)
2002 Functional & Integrative Genomics  
A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.  ...  Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming  ...  Acknowledgements We would like to thank the TAIR users and the Arabidopsis research community for their continuing support, feedback, and particularly for sharing their data and expertise.  ... 
doi:10.1007/s10142-002-0077-z pmid:12444417 fatcat:tolsqcyr6rfudawr6ozmlxcely
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