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NEW TOOLS

Fusariuim Protein Toolkit A set of tools and datasets to explore the functions and structures of the Fusarium proteome.

Phylostrata Phylostratigraphy determines the level of evolutionary conservation of a given protein.

PanEffect PanEffect: A tool to explore the variant effects across the maize pan-genome.

SNPversity 2.0 A tool to access large-scale maize genetic variation data.

Foldseek Search Fast comparisons of large protein structure sets.

FATCAT Comparison Shows the structural alignments between a query maize protein with the top hits from the sequence-based tool Diamond and two structural alignment tools FoldSeek and FATCAT.

NEW DATASETS

Genome datasets from the Amaizing project
More information

Cell type-specific cis regulation in maize.
More information

New Phylostrata browser tracks.
More information

Highland-lowland project genome datasets
More information

Information about the international maize community

The Maize Genetics Conference: Information about past, present, and future Annual Maize Genetics Conference.
The Maize Newsletter: An archive of all issues of the Maize Newsletter, dating back to 1929.
Jobs: Job opportunities that have been shared with MaizeGDB.
Find researchers: Find maize researchers.
A history of maize: A summary of the development of cultivated maize from the Ross-Ibarra lab.
A timeline of maize research: Explore a timeline of maize research and resources, including history of MaizeGDB.
Editorial board: A volunteer group of four to five researchers who recommend one paper each month.
Maize nomenclature recommendations: Consistent nomenclature is essential to FAIR (Findable, Accessible, Interoperable and Reuseable) data.
Videos: A collection of videos, including note-worthy talks and maize pollination demonstrations.
Project documentation: A few important maize research projects are described in pages maintained at MaizeGDB.

A century of maize cooperation

Cooperators page
The Maize Genetics Cooperation: An organization to facilitate progress in maize research through collaboration and cooperation.
Classic papers: A list of some of the most influential papers on maize genetics.

Complete list of research tools

BLAST: Sequence search against the full set of genome datasets hosted at MaizeGDB.
Bin Viewer: Explore data in regions defined by genetic boundaries.
CornCyc: Metabolic pathways resource for maize.
FATCAT Comparison Tool: Structural alignments between a maize protein with the top hits from Diamond and the structural alignment tools FoldSeek and FATCAT.
FoldSeek Search: Fast comparisons of large protein structure sets.
Fusarium Protein Toolkit: Tools and datasets to explore the functions and structures of the Fusarium proteome.
GBrowse genome browsers: An older genome browser, which hosts older genome assemblies, including B73v1, B73v2, B73v3, B73v4, NRGene W22v2, and few other older datasets.
JBrowse genome browsers: The GBrowse replacement, which hosts B73v5 along with most of the assemblies hosted at MaizeGDB.
GenomeQC: A tool to assess genome and gene model annotation quality.
Genome Context Viewer: A web application for explore gene families in their genomic context across multiple maize genome assemblies.
Maize Feature Store: A centralized repository of updated, raw and transformed data collected from multiple sources. Suitable for Machine Learning.
MaizeMine: An integrated data warehouse for MaizeGDB.
Newly characterized genes: Browse newly characterized genes.
PanEffect: Explore variant effects across the maize pan-genome.
Pathway Association Study Tool (PAST): Assigns SNPs to genes and genes to metabolic pathways.
PedigreeNet: Explore pedigree networks for maize accessions hosted by MaizeGDB.
Phylostrata: Phylostratigraphy determines the level of evolutionary conservation of a given protein.
Protein structures: Explore predicted gene model proteins. Includes Foldseek search, FATCAT comparisions and protein structure predicted by AlphaFold and MetaAI ESMFold.
qTeller: A comparative RNA-seq expression platform to compare expression across multiple data sources.
SNPversity 2.0: Create a VCF file based on a given region of the B73 genome and a subset of diverse maize accessions.
TYPSimSelector: Sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa)

Older tools that are still live at MaizeGDB

Incongruency tool: Shows inconsistent genomic order in the B73 v2 assembly, as compared to the IBM 2009 genetic map.

About MaizeGDB

Cite us
Contact us
NCGA podcasts (2012-2013)
FAQs

Common tasks

How to name entities in your data
How to contribute genomic data
How to contribute data to MaizeGDB
Submit an assembly to GenBank
Submit an assembly to ENA

Curated data types at MaizeGDB

Individual data types curated from research papers

Alleles/Polymorphisms
SNPs and Traits
Expression
Gene/Gene Models
Genome datasets
Gene Products
Images
Loci + QTL
Maps
Metabolic Pathways
Molecular Markers
Pan-genes
Phenotypes
Protein structures
References
Stocks

Archived data at MaizeGDB

MaizeGDB has a policy of not deleting data. The database holds data that was generated in the 1920s and earlier, up to the current time. But some of that data is rarely used, and so is available only through archived pages. These are listed below.
Note that these data centers may degrade over time.

BACs
Cytogenics
ESTs
Overgoes
Recombination maps

Welcome to MaizeGDB!

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Helpful Links

Maize genetics community

Maize Genetics Cooperation - MGC

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Resources

Maize Genetics Meeting

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