This site provides sequence and annotation of the Zea mays ssp. mays genome resulting from the Maize Genome Sequencing Project. The browser is based on the July 2005 release of the AGI Agarose FPC Map and on BAC clone sequences contained therein.
Sequencing of the B73 cultivar commenced in November 2005 as part of a 3-year multi-institutional collaboration funded jointly by the NSF, USDA, and DOE. The strategy is to individually sequence a set BAC clones across a minimum-tiling path. Gene space will be identified and sequenced to finished quality. Read more about the Maize Genome Project or view the current sequencing progress.
Our goal is to provide convenient entry points into the maize genome both by searching and browsing, and to display salient features, including predicted genes, markers, repeats, and expressed and conserved regions. This goal will be accomplished in phases over the 2006-2007 time-frame.
As we strive to improve MaizeSequence.org and turn it into an invaluable community resource, we invite users to provide us with feedback about the site. We welcome any comment, question, or feature request that you may have.
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 (FgenesH), alignment to EST, cDNA, and GSS sequences, as well as repeats. Over time a given BAC sequence will acquire Secondary Annotations, linking its features to comparative maps (CMap), orthologue/paralogue/synteny analysis (Compara), and protein sequence characterization (InterPro/GO). 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. Presently, ContigView is available for external BAC clones that have been sequenced prior to the Maize Genome Project. Newly processed clones will become available in ContigView starting January, 2007.
The following features are enhancements over the maize browser in Gramene:
The following is a list of features that we are currently developing: