Browser Views

View the genome at varying levels of resolution. The maize genome browser is built on the EnsEMBL browser, which provides a rich set of genome displays and data access functionality. The various views are tightly interlinked, both internally and through deep links to other genome browsers, resulting in easy and intuitive navigation.

MapView: Based on the physical map, displays the genome at the fingerprint contig level. This view also shows "virtual bins", which are correspondences to core bins, based on anchored genetic markers. Histogram-like overviews display the density of markers, clones, and accessioned sequences.

CytoView: A detailed view of the physical map, displays the position of BAC clones and hybridized markers. Clones that are sequenced and submitted to GenBank are color coded depending on their source and extent of annotation. Simple sequence repeats detected in BAC-end sequences are also annotated.

ContigView: Based on the BAC sequence, displays Primary Annotations, including ab initio gene prediction, alignment to known data sets, and repeat annotations. Over time BAC sequences will acquire Secondary Annotations, where evidence-based analysis is used to validate and enrich primary features. The extent of annotation available for a particular clone is indicated by color code within CytoView. ContigView is available only for BAC clones that have reached HTGS_IMPROVED status, in which genic regions are of finished quality. ContigView is also available for external BAC clones that have been sequenced prior to the Maize Genome Project.

SyntenyView: Provides a graphical display of the syntenic relationships between the maize genome and other cereal genomes. We currently provide chromosome-level displays for maize against rice. Contextual menus provide jumping points for maize views on this browser and for rice genome views on the Gramene browser.

GeneView: Provides a full report of gene structure and mapped annotations for predicted maize genes. The gene-centric displays provide a wide array of information for a given gene or its neighbors.