| Chapter title |
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
|
|---|---|
| Chapter number | 7 |
| Book title |
Plant Bioinformatics
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-3167-5_7 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-3166-8, 978-1-4939-3167-5
|
| Authors |
Tello-Ruiz, Marcela Karey, Stein, Joshua, Wei, Sharon, Youens-Clark, Ken, Jaiswal, Pankaj, Ware, Doreen, Marcela Karey Tello-Ruiz, Joshua Stein, Sharon Wei, Ken Youens-Clark, Pankaj Jaiswal, Doreen Ware |
| Editors |
David Edwards |
| 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. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 25% |
| Unknown | 3 | 75% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 75% |
| Scientists | 1 | 25% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | 9% |
| Italy | 1 | 9% |
| Unknown | 9 | 82% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 3 | 27% |
| Student > Bachelor | 3 | 27% |
| Student > Postgraduate | 2 | 18% |
| Student > Ph. D. Student | 2 | 18% |
| Other | 1 | 9% |
| Other | 0 | 0% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 9 | 82% |
| Biochemistry, Genetics and Molecular Biology | 1 | 9% |
| Environmental Science | 1 | 9% |