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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 www.ebi.ac.uk/arrayexpress Archive for functional genomics data from microarray and sequencing platforms
BarleyGenes https://ics.hutton.ac.uk/barleyGenes/ Gene and RNA-seq database for Barley
Chrysanthemum Transcriptome Database http://www.icugi.org/chrysanthemum Database of chrysanthemum’s gene and transcripts
Cottongen https://www.cottongen.org/ Genomics, genetics, and breeding database for cotton
Expression Atlas EMBL-EBI www.ebi.ac.uk/gxa/home Open resource platform for gene and protein expression information
Ensembl Plants https://plants.ensembl.org/index.html Genomic database (genome sequence, gene models, functional annotation) of more than 33 plant species
Gene Expression Omnibus www.ncbi.nlm.nih.gov/projects/geo Functional genomics data repository
MaizeDIG https://maizedig.maizegdb.org/ Genotypic-phenotypic database for maize
MaizeGDB https://www.maizegdb.org/ Genetic and genomics database for maize
MaizeMine https://maizemine.rnet.missouri.edu/maizemine/begin.domine/begin.do Archive to access literature, genomic, interaction and proteomic data for maize
VvGDB www.plantgdb.org/VvGDB/ Database for grape genome
Phytozome https://phytozome-next.jgi.doe.gov/ Comparative genomics portal of plants
Plant Promoter Database http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom Database of plant promoter sequences and experimentally determined transcription start site of various plant species
PLEXdb http://www.plantgdb.org/prj/PLEXdb/ Plant expression database with gene expression profile data sets, structural genomics, and phenotypic data
Pomamo https://www.gabipd.org/projects/Pomamo/ Archive of potato sequences, literature, maps, and tools
PRGdb http://prgdb.org/prgdb/ Archive of pathogen receptor genes of various plant species
Rice Expression Database http://expression.ic4r.org/ Repository of gene expression profiles of rice from RNA-seq data on tissues spanning an entire range of rice growth
Rice expression profile Database http://ricexpro.dna.affrc.go.jp/ Repository of gene expression profiles of rice from microarray analysis
SolGenomics Network https://solgenomics.net/gem/experimental_design.pl?id=2 Database and tool of genomics and genetics approach for tomato and some other plant species such as eggplant
TAIR https://www.arabidopsis.org/ Database of genetic and molecular biology data for Arabidopsis thaliana
The Rice Annotation Project Database https://rapdb.dna.affrc.go.jp/ Archive of rice genome sequence, structure, and function
Tomato Functional Genomics Database http://ted.bti.cornell.edu Archive of tomato microarray data, metabolite and RNA-seq
Metabolomic Database Metabolights www.ebi.ac.uk/metabolights/ Metabolomics database (cross-species, metabolite structures, biological role)
Pathway Database Reactome www.reactome.org Pathway interaction repository
RiceCyc http://pathway.gramene.org/gramene/ricecyc.shtml Database of known and predicted biochemical pathways from rice
PlantCyc http://plantcyc.org Metabolic pathway reference database from over 350 plant species
RNA Analysis Tool qTeller https://qteller.maizegdb.org/ Comparative RNA-seq expression tool
Chemical Compound Database ChEBI www.ebi.ac.uk/chebi/ Archive of molecular entities that focuses on small chemical compounds
PubChem http://pubchem.ncbi.nlm.nih.gov/ Archive of chemical information of various chemical compounds
Mass Spectrum Database ReSpect for Phytochemicals http://spectra.psc.riken.jp/menta.cgi/index Database for phytochemicals MS spectra data and literature
Metlin http://metlin.scripps.edu/ Comprehensive MS/MS database
Resistance Analysis Disease Resistance Analysis and Gene Orthology (DRAGO2) http://prgdb.org/prgdb/drago2 Annotate resistance genes
Networking and Interaction Analysis PathoPlant www.pathoplant.de/ Database of plant-pathogen interaction and components related to plant pathogenesis
AraNet www.inetbio.org/aranet/ Probabilistic functional gene network tool for Arabidopsis thaliana
PLANET http://aranet.mpimp-golm.mpg.de/ Platform for visualization and analysis of co-function networks of photosynthetic organisms
Genomics Tool The Bio-Analytic Resource http://bar.utoronto.ca/ Plant bioinformatics tools resource platform (gene expression, mapping, molecular markers, and genomics)