Tello-Ruiz, M. K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (January 2016) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol, 1374. pp. 141-63. ISSN 1940-6029 (Electronic)1064-3745 (Linking)
Abstract
Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. 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. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.Moreover, this is the first publication describing Gramene's new web interface-intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Comparative genomics Gene homology Genetic variation Phylogenetics Plant genome Plant pathways Reference genomes Structural variation Synteny |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics 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 2016 |
| Date Deposited: | 09 Nov 2015 19:47 |
| Last Modified: | 09 Nov 2015 19:47 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31967 |
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