MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and
model organism Zea mays.
MaizeGDB is a founding member of
AgBioData,
a consortuim of agriculture-related online resources which is
committed to making agriculture-related research data FAIR.
TYPSimSelector: A tool that 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).
GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
Due to lack of resources, the tools for searching for data objects
(e.g. stock records, publications) via sequence have not been updated
to work with the current genome assemblies and data sets, which means
they can produce misleading results. As a result, these tools have been
discontinued until further notice.
Search shortcuts
Search for
maize projects and resources Use the search options on the main search
page or check the left-hand menu for short cuts to some specific types of
projects and resources.
Find
mutant alleles: Starting with your sequence,
search for seed stock from the UniformMu, TILLING, and other projects
containing mutant alleles in your gene of interest. The link will provide
the correct settings for this search.
Find
publications associated with your sequence:
POPcorn will check multiple sources to see if your sequence, or a similar
sequence is associated with a publication. The link will provide
the correct settings for this search.
Align
your sequence on genome browsers: POPcorn will align
your sequence on assemblies, including the B73 genome and Maize Assembled
Genomic Islands, using BLAST. Where possible, the BLAST hits will be
uploaded as a custom track. The link will provide
the correct settings for this search.
BLAST against multiple datasets:
Find matching or similar sequences by BLASTing against many maize data
sets available on the web.
See
the full list of sequence-indexed searches See
the full list of BLAST data sets
POPcorn has been integrated into the MaizeGDB.
Work on POPcorn began in February of 2009. Prior to being integrated
into the MaizeGDB website, it was be released in three phases over
two years.
Phase 1
Provide a searchable database of maize projects and resources.
Completed in April 2009. Data is updated monthly and information
about new projects can be submitted.
Phase 2
Provide tools for sequence-based searching of participating maize
projects and resources.
– Released in April, 2010. Improvements and additional
functionality updated multiple times a year.
– The POPcorn BLAST utility became the main MaizeGDB.org BLAST
utility in fall 2011.
– CViT (Chromosome Viewing Tool) has been re-developed for use
in MaizeGDB.org and POPcorn for visualizing data.
Phase 3
Provide tools and processes to enable projects to transition
their data to MaizeGDB when the projects are complete.
POPcorn was funded by NSF, award
#0743804
with in-kind contributions from USDA-ARS.
The poster from the PAG XIX (January, 2011) is
here.
The PowerPoint presentation from the PAG XIX (January, 2011)
meeting is here.
The poster from the March, 2010 Maize Meeting is
here
