The Maize Genome Browser

Welcome to MaizeSequence.org

This site provides full access to the latest sequence data and primary annotations of the maize genome.

Browse the genome visually through our Ensembl-driven genome browser [More Information].
Search for specific maize data through a unified feature name search (top-right-hand corner) or through our BLAST server.
Download entire data sets via FTP.
Get notified when new data arrives through our RSS notification system.

New to the site? Get started on the project overview page.

Maize golden path (AGP v1) available for download

The maize accessioned golden path (AGP), consisting of 10 chromosome pseudo-assemblies guided by the physical map, is available for download through the Arizona Genomics Institute [AGI homepage]. The data is available both as chromosome sequences (FASTA format) as well as tabulated information (AGP file) describing how the chromosomes are assembled from component BAC clones. We are working on integrating the golden path into the MaizeSequence.org genome browser and intend to include it as part of Release 4a.53.

See the project from beginning to end!

As part of the project's education outreach, we have produced, in conjunction with the Dolan DNA Learning Center, an exciting interactive tutorial, featuring interviews and demos about the sequencing effort, public access to the data, and its impact on science and agriculture. [Visit DNALC]

Gene annotations for Release 3b.50

Putative protein-coding genes are annotated using two methods in the current release. Ab initio predictions were performed using Fgenesh (monocot) on repeat-masked sequence, and are displayed in the track "Fgenesh (masked)". Genes from this set are color-coded to indicate homology to GenBank proteins (blue for homology versus gray for none) and to distinguish genes encoded by transposable elements (red). The second method used evidence from FL-cDNA, EST, and proteins (see FAQ for details); resulting annotations are displayed in the track "GeneBuider". The track labeled "Working Gene Set" is a combination of GeneBuilder genes and non-overlapping Fgenesh models. These were subjected to both InterPro domain searches and to Gene Ontology (GO) assignment. The track "Filtered Set" is derived from the "Working Gene Set", screened to remove pseudogenes, TE-encoded genes, low-confidence hypothetical genes, and flawed annotations. In the next release we will implement improvements to the evidence-based method and will provide Fgenesh annotations on newly available BAC sequences.

News

Download the Filtered Gene Set
The Filtered Gene Set (FGS) is now available on our FTP site. We are still working hard to release the new site with the chromosome assemblies as part of the browser, but in the meantime we wanted to share a definitive set of genes that were annotated and validated by cross-species analysis.
Delay of Release 4a.53
Release 4a.53 is being delayed and will be made available at the end of June, instead of April 29, 2009. We apologize for any inconvenience that this may cause. Read more about the delay as well as our intentions for the release here.
Download the maize golden path
The maize golden path (AGP v1) can be accessed in FASTA and AGP formats from the Arizona Genomics Institute.
Intentions for Release 4a.53
Release 4a.53 is expected on ~~April 29, 2009~~ May 27, 2009. The release will include, among others, a maize genome golden path, an improved working gene set, and a new version of the browser. Read more about our intentions for the release here.
Tour the Project!
Experience an interactive demo covering many aspects of the sequencing project.
Release 3b.50 (February, 2009)
An incremental annotation-based release that includes a new filtered gene set and several website enhancements
Filtered Gene Set
A subset of the Working Gene Set that has been filtered to remove pseudogene, TE-encoded genes, and partial models
Updated FTP dumps
The FTP site has been reorganized to provide different data sets in a variety of formats. All gene sequence dumps now include CDS sequences as well.
We're now on Twitter!
You can keep up with the latest news and bulletins by following us on Twitter, or read updates from the left navigation bar.
Reorganized menus
Menus on the BAC-based genome browser have been simplified and standardized with the Gramene genome browser.

Older News

Release 2a.50 (October, 2008)
The current release of the maize sequence features DNA and annotation of 16,205 BACs, including over 4,000 BAC updates. An evidence-based gene build is presently in progress and should be available at the end of October. For more information, please refer to the release page.
Functional annotations now available
Functional annotations, including Gene Ontology (GO) and other descriptions of specific genes, are now computed by the Xref system
Release 3a.50 (December, 2008)
This release of the maize sequence includes DNA and annotation of 16,587 BAC clones. It includes close to 3 billion bases of maize sequence. Over the course of 2009 we will continue to work on gap-filling sequences and to provide important annotation builds and data updates. For example, in the next 3 months we expect to release, in close collaboration with Gramene, fully-annotated phylogenetic trees describing evolutionary relationships among maize, rice, and sorghum gene orthologues. You can find more information about the current release as well as a short-term website roadmap on our release page.
The Working Gene Set
Release 3a.50 features a set of non-overlapping genes that cover the entire maize genome. The set consists of over 90,000 evidence-based genes computed by the Gramene GeneBuilder, complemented by a set of more than 20,000 ab initio Fgenesh predictions that were computed on RepeatMasked sequence whose loci are not covered by the evidence-based set
BLAST server improvements
We have made several performance-related and visual enhancements to BlastView. These improvements should restore stability of the BLAST functionality