TY - ECHAP
AU - Marcela Tello-Ruiz
AU - Joshua Stein
AU - Sharon Wei
AU - Ken Youens-Clark
AU - Pankaj Jaiswal
AU - Doreen Ware
AB - 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.
BT - Methods in molecular biology (Clifton, N.J.)
C1 - http://www.ncbi.nlm.nih.gov/pubmed/26519404?dopt=Abstract
DA - 2016
DO - 10.1007/978-1-4939-3167-5_7
J2 - Methods Mol. Biol.
LA - eng
N2 - 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.
PY - 2016
SP - 141
EP - 63
T2 - Methods in molecular biology (Clifton, N.J.)
TI - Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
VL - 1374
SN - 1940-6029
ER -