01595nas a2200205   4500000000100000000000100001008004100002260000900043100002300052700001700075700001500092700002100107700001900128700001600147245008100163300001100244490000900255520111100264022001401375       2016                            d  c20161 aMarcela Tello-Ruiz1 aJoshua Stein1 aSharon Wei1 aKen Youens-Clark1 aPankaj Jaiswal1 aDoreen Ware00aGramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.  a141-630 v13743 aGramene 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.  a1940-6029