Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

Table 2

List of databases and their information of application to crop plant research community.

Name of databases	Application
AgBase—a unified resource for functional analysis in agriculture	Search and analyze functional genomics datasets in agricultural species
AutoSNPdb—an annotated single nucleotide polymorphism database for crop plants	Identify SNPs from assembled EST sequences for the crops rice, barley, and Brassica
BarleyBase—an expression profiling database for plant genomics	Analyze and visualize plant microarray data
BBGD—an online database for blueberry genomic data.	It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function
BIOGEN BASE—CASSAVA	A web accessible resource for investigating cassava phenomics and genomics information
CastorDB—a comprehensive knowledge base for Ricinus communis.	CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data, and protein interacting partners
ChromDB—The Chromatin Database	Locate chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms
CR-EST—a resource for crop ESTs	Search for sequence, classification, clustering, and annotation data of crop EST projects
CSRDB—a small RNA integrated database and browser resource for cereals	Search for sequence information on rice, maize, and other cereal crops small RNAs
DEBDOM—Database Exploring Banana Diversity of Manipur	The database DEBDOM provides a sophisticated web base access to the details of the taxonomy, morphological characteristics, utility, and sites of collection of Musa genotypes
DRASTIC—Database Resource for the Analysis of Signal Transduction in Cells	Search for information of plant gene expression in response to pathogens and environmental changes
FLAGdb++—A Database for the Functional Analysis of the Arabidopsis Genome	Search and visualize data for high-throughput functional analysis of Arabidopsis, rice, and other plant genomes
GabiPD—a plant integrative “omics” database	Search for comprehensive and extensive information on various plant genomes generated by a German collaborative network of plant genomics research
GCP—The Generation Challenge Programme	An online resource documenting stress-responsive genes comparatively across plant species
GDR—Genome Database for Rosaceae	A central repository of curated and integrated genetics and genomics data of Rosaceae, which includes apple, cherry, peach, pear, raspberry, rose, and strawberry
GeneCAT—gene co-expression analysis toolbox	Novel web tools that combine BLAST and coexpression analyses
GeneSeqer@PlantGDB—gene structure prediction in plant genomes	Predict gene structures of plant genomes
GERMINATE	A generic database for integrating genotypic and phenotypic information for plant genetic resource collections
GGT—Graphical GenoTypes	Software for visualization and analysis of genetic data
GrainGenes—The genome database for small-grain crops	Search for molecular and phenotypic information on wheat, barley, rye, triticale, and oats
Gramene—a resource for comparative grass genomics	Curated resource for genetic, genomic, and comparative genomics data for the major crop species, including rice, maize, wheat, and many other plant (mainly grass) species
MaizeGDB—the Community Database for Maize Genetics and Genomics	Search genetic and genomic information about maize
MANET—The Molecular Ancestry Network	Tracing evolution of protein architecture in metabolic networks
Medicago—A database for personalized data mining of the model legume Medicago truncatula transcriptome	Search for integrated genomic, genetic, and biological information on cool season legume Medicago truncatula (Mt)
MetaCrop—a detailed database of crop plant metabolism	A database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models
MetaCrop 2.0—managing and exploring information about crop plant metabolism.	It contains information about seven major crop plants with high agronomical importance and two model plants; MetaCrop is intended to support research aimed at the improvement of crops for both nutrition and industrial use
Narcisse—a mirror view of conserved syntenies	A database dedicated to the study of genome conservation
NIASGBdb—National Institute of Agrobiological Sciences Gene Bank DataBase	Find information about agricultural plant genetics and diseases
P3DB—Plant Protein Phosphorylation Database	Find information about protein phosphorylation in plants
Panzea—a database and resource for molecular and functional diversity in the maize genome	Search for information on relationship between genotype and functional phenotype variations
Pepper EST database—in silico exploitation of EST data to extensively score genes of Capsicum annuum	Comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome
PIP—a database of potential intron polymorphism markers	A database of potential intron polymorphism markers in plants
PLACE—plant cis-acting regulatory DNA elements	Search for documented motifs found in plant cis-acting regulatory DNA elements
Plant snoRNA database	Search for comprehensive information on small nucleolar RNAs in plants
PlantCARE—a database of plant cis-acting elements	Search for information on plant cis-acting regulatory elements, transcription sites, enhancers, and repressors
PlantTFDB—Plant Transcription Factor Databases	A comprehensive plant transcription factor database
PlantTribes—a gene and gene family resource for comparative genomics in plants	A plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa, and Populus trichocarpa
PLecDom—Plant Lectin Domains server	Find information about plant lectin domains
PlnTFDB—Plant Transcription Factor Database	Find information about transcription factors in plants
PmiRKB—Plant MicroRNA Knowledge Base	Find information about plant microRNAs
PMRD—Plant MicroRNA Database	Find information about microRNA sequences and targets in plants
PODB—the Plant Organelles Database	Search a collection of visualized plant organelles and protocols for plant organelle research
POGs/PlantRBP—a resource for comparative genomics in plants	Search for information on putative orthologous proteins among rice, maize, and Arabidopsis with emphasis on RNA-binding proteins
PoMaMo—a comprehensive database for potato genome data	Search for comprehensive genomic information on potato
PREP Suite—Predictive RNA Editor for Plants	Use to predict sites of RNA editing in plants
PRGDB—Plant Resistance Genes DataBase	Find information about genes involved in plant defense mechanisms
pssRNAMiner—a plant short small RNA regulatory cascade analysis server	Identify both the clusters of phased small RNAs as well as the potential phase-initiator
RadishBase—a database for genomics and genetics of radish.	A database containing radish pathways predicted from unigene sequences is also included in RadishBase
RoBuST—an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae.	The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV (root and bulb vegetables) researchers
SALAD—Surveyed contained motif ALignment diagram and the Associating Dendrogram	Perform systematic comparison of proteome data among species
SGN—SOL Genomics Network	A comparative map viewer dedicated to the biology of the Solanaceae family
Shanghai RAPESEED Database—a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica	Find information on EST, gene expression profiles, and bioresources for the promotion of functional genomics studies and quality breeding of Brassica crops
SolRgene—an online database to explore disease resistance genes in tuber-bearing Solanum species	The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota
SoyBase—USDA-ARS soybean genetics and genomics database	Find genetic information about soybeans
SoyTEdb—a comprehensive database of transposable elements in the soybean genome.	SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date
SoyXpress—a database for exploring the soybean transcriptome	A soybean gene expression and transcription database
Sputnik—a database platform for comparative plant genomics	Search for ESTs from over 20 different plant species
TFGD—Tomato Functional Genomics Database	Find information about tomato genes
The Adaptive Evolution Database (TAED)—a phylogeny based tool for comparative genomics	Search for information on adaptive evolution in gene families of higher plants and chordate
The Legume Information System (LIS)—an integrated information resource for comparative legume biology	Search for integrated genetic and molecular data from multiple legume species
The Plant DNA -values Database	Search for information on plant DNA -values and genome sizes
The Plant Ontology Database—a resource for plant structure and developmental stages	View, search, and query plant ontology terms
The PlantsP Functional Genomics Database	Search for information on plant kinases and phosphatases
The TIGR Maize Database	Search for annotated genomic sequences of maize
The TIGR Plant Repeat Databases—A Collective Resource for the Identification of Repetitive Sequences in Plants	Identify, classify, and analyze repetitive sequences in plant genomes
TomatEST database—in silico exploitation of EST data to explore expression patterns in tomato species	Find expressed sequence tag (EST)/cDNA sequence information from different libraries of multiple tomato species
TriMEDB—a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae.	The Triticeae mapped expressed sequence tag (EST) database
TropGENE-DB—A Multi-tropical Crop Information System	Search for genetic, molecular, and phenotypic data of tropical crop species
TropGENE-DB—A Multi-tropical Crop Information System	Search for genetic, molecular, and phenotypic data of tropical crop species
UK CropNet—a collection of databases and bioinformatics resources for crop plant genomics	Search sequences and genomic information on crop plants
WhETS—Wheat Estimated Transcript Server	A tool to provide the best estimate of hexaploid wheat transcript sequence