Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., Ware, D. (January 2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048
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Abstract
Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Crops, Agricultural/genetics *Databases, Genetic Genetic Variation *Genome, Plant *Genomics Internet Metabolic Networks and Pathways/genetics Molecular Sequence Annotation Plants/genetics/metabolism |
| Subjects: | bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > databases > databases bioinformatics > genomics and proteomics > datasets bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab |
| Depositing User: | Matt Covey |
| Date: | January 2014 |
| Date Deposited: | 11 Apr 2014 18:45 |
| Last Modified: | 11 Apr 2014 18:45 |
| PMCID: | PMC3964986 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/29750 |
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