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Table 1 List of bioinformatics databases and tools applied in plant biotechnology

From: Bioinformatics approaches and applications in plant biotechnology

Function Servers URL Details
Genome Database ArrayExpress Archive for functional genomics data from microarray and sequencing platforms
BarleyGenes Gene and RNA-seq database for Barley
Chrysanthemum Transcriptome Database Database of chrysanthemum’s gene and transcripts
Cottongen Genomics, genetics, and breeding database for cotton
Expression Atlas EMBL-EBI Open resource platform for gene and protein expression information
Ensembl Plants Genomic database (genome sequence, gene models, functional annotation) of more than 33 plant species
Gene Expression Omnibus Functional genomics data repository
MaizeDIG Genotypic-phenotypic database for maize
MaizeGDB Genetic and genomics database for maize
MaizeMine Archive to access literature, genomic, interaction and proteomic data for maize
VvGDB Database for grape genome
Phytozome Comparative genomics portal of plants
Plant Promoter Database Database of plant promoter sequences and experimentally determined transcription start site of various plant species
PLEXdb Plant expression database with gene expression profile data sets, structural genomics, and phenotypic data
Pomamo Archive of potato sequences, literature, maps, and tools
PRGdb Archive of pathogen receptor genes of various plant species
Rice Expression Database Repository of gene expression profiles of rice from RNA-seq data on tissues spanning an entire range of rice growth
Rice expression profile Database Repository of gene expression profiles of rice from microarray analysis
SolGenomics Network Database and tool of genomics and genetics approach for tomato and some other plant species such as eggplant
TAIR Database of genetic and molecular biology data for Arabidopsis thaliana
The Rice Annotation Project Database Archive of rice genome sequence, structure, and function
Tomato Functional Genomics Database Archive of tomato microarray data, metabolite and RNA-seq
Metabolomic Database Metabolights Metabolomics database (cross-species, metabolite structures, biological role)
Pathway Database Reactome Pathway interaction repository
RiceCyc Database of known and predicted biochemical pathways from rice
PlantCyc Metabolic pathway reference database from over 350 plant species
RNA Analysis Tool qTeller Comparative RNA-seq expression tool
Chemical Compound Database ChEBI Archive of molecular entities that focuses on small chemical compounds
PubChem Archive of chemical information of various chemical compounds
Mass Spectrum Database ReSpect for Phytochemicals Database for phytochemicals MS spectra data and literature
Metlin Comprehensive MS/MS database
Resistance Analysis Disease Resistance Analysis and Gene Orthology (DRAGO2) Annotate resistance genes
Networking and Interaction Analysis PathoPlant Database of plant-pathogen interaction and components related to plant pathogenesis
AraNet Probabilistic functional gene network tool for Arabidopsis thaliana
PLANET Platform for visualization and analysis of co-function networks of photosynthetic organisms
Genomics Tool The Bio-Analytic Resource Plant bioinformatics tools resource platform (gene expression, mapping, molecular markers, and genomics)