Food Crops: Cereals, Grains, and Grasses
BarleyBase-A community resource for cereal microarrays
http://www.plexdb.org/plex.php?database=Barley
BarleyBase is a public repository for plant microarray data. In addition
to experiment and expression data, links to PlantGDB and Gramene allow users
to perform gene predictions or cross-species comparisons at the genome level.
BarleyBase is expanding to become PLEXdb, the comprehensive Plant Expression
Database.
CR-EST: Crop Expressed Sequence Tag Database (IPK-- Institute of Plant
Genetics and Crop Plant Research)
http://pgrc.ipk-gatersleben.de/cr-est/index.php
The site provides access to sequence, classification, and taxonomic data for
several plant species (mostly barley, but also it includes some data for wheat,
pea, potato, and tobacco). EST sequences are clustered and analyzed against
model plant genes and available data includes consensus sequence, functional
annotations, and expression data. Entries also include cross-links to relevant
external web sites.
GrainGenes: A database for Triticaceae and Avena
http://rye.pw.usda.gov/cmap/
This database provides access to genetic and genomic data for Triticaceae and Avena species:
wheat, barley, rye, oat, and their wild relatives. Curated data is provided
for genetic and physical maps, genes, and QTL information. Other types of data
include sequences (EST, genomic, and contiq assemblies), gene products, taxonomies,
and literature citations. GrainGenes also includes links to corresponding records
in other resources (GenBank, Unigene, BarleyBase, and others).
Gramene: A Resource for Comparative Grass Genomics
(Cold Spring Harbor and Cornell University)
http://www.gramene.org/
Gramene is a curated
database containing the complete genome sequences for Arabidopsis,
maize, and rice. The protein section of the database provides information on
SwissProt-TrEMBL protein entries from family Poaceae (Grasses). Genetic
and physical maps, and a comparative map viewer, are available for rice, maize,
wheat, barley, oats, sorghum, and other grasses. Other information includes
markers, a QTL database, SNPs, pathway information, and literature citations.
HarvEST (University of California, Riverside)
http://harvest.ucr.edu/
HarvEST is a tool for viewing ESTs with support for identifying gene function,
functional annotation, mapping, comparative genomics, and microarray design.
EST sequences in HarvEST have been quality trimmed, cleaned, and assembled
into unigenes. Putative gene function is based on BLASTX hits from the GenBank
translated nr database, and from the annotated rice and Arabidopsis genomes.
The database also contains links to other sequence databases and facilitates
connection to NCBI for BLAST searches of the public dbEST database. Both HarvEST
wheat and barley include viewing functions for the associated Affymetrix GeneChip®.
Species included in HarvEST include wheat, barley, citrus, soy, cowpea, and
coffee.
OryzaBase
http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp
The OryzaBase is intended to be a comprehensive rice science database covering
knowledge ranging from classical rice genetics to genomic analyses. OryzaBase
has several components, including genetic stock information, a gene dictionary,
and chromosome maps. The database contains over 13,000 strain entries, almost
5,000 marker entries, over 2000 trait genes, and almost 3,000 references. The
current focus of OryzaBase is to provide cross-references to major DNA sequence
databases, literature citations, and other plant databases.
MaizeGDB—Maize Genetics and Genomics Database
http://www.maizegdb.org/
MaizeGDB is a community resource for biological information about Zea
mays ssp. mays. The site provides access to genetic, genomic, sequence,
gene product, functional characterization, literature reference, and person/organization
contact information. The site also includes maps, metabolic pathways, and
polymorphisms.
Panzea
http://www.panzea.org
Panzea
provides access to data and tools for the analysis of molecular and functional
diversity in maize. The database contains genotype, phenotype, and polymorphism
data from the Maize Diversity Program. Panzea also includes a bibliography on
maize evolution and diversity; with links to text when available.
TIGR Rice Genome Annotation
http://www.tigr.org/tdb/e2k1/osa1/
The TIGR Rice Genome Annotation Database provides sequence and annotation
data for the 12 rice chromosomes. The Genome Browser provides an integrated
display of annotation data.
Whole Rice Genome Automated Annotation Database
http://www.tigr.org/tdb/e2k1/osa1/irgsp.shtml
This database contains rice sequences processed through an automated
annotation pipeline. Sequences can be searched by gene name, clone name,
and locus identifier. In addition, the table of clones is sorted by chromosome
and by map position on the chromosome to facilitate browsing. A domain
search locates sequences containing Pfam domains and Interpro database
hits.
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