title: Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
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.
authors.affiliation: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Marcela Karey
authors.initials: MK
authors.lastname: Tello-Ruiz
authors.affiliation: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Stein
authors.affiliation: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Sharon
authors.initials: S
authors.lastname: Wei
authors.affiliation: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Youens-Clark
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.affiliation: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA. ware@cshl.edu.|USDA-ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, 14853, USA. ware@cshl.edu.
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction; D012984:Software; D064878:Web Browser
keywords: Comparative genomic s; Gene homology; Genetic variation; Phylogenetics; Plant genome; Plant pathway s; Reference genome s; Structural variation; Synteny