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In the context of plant breeding, bioinformatics can empower genetic and genomic selection to determine the optimal combination of genotypes that will produce a desired phenotype and help expedite the isolation of these new varieties. Bioinformatics is also instrumental in collecting and processing plant phenotypes, which facilitates plant breeding. Robots that use automated and digital technologies to collect and analyze different types of information to monitor the environment in which plants grow, analyze the environmental stresses they face, and promptly optimize suboptimal and adverse growth conditions accordingly, have helped plant research and saved human resources.
URL |
Note |
Description |
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http://bigd.big.ac.cn/databasecommons/ Accessed on 4 May 2022. |
Comprehensive publicly available data repository covering a wide range of organisms |
Bigd database consolidates all the information collected about the database. Each database is classified by data type, category, subject, and location, so that people can easily find a specific collection of databases of interest. |
Accessed on 4 May 2022. |
Covers a wide range of biological research databases and software tools |
Expasy database is divided into several areas: DNA, RNA, protein, population, cell, etc. According to omics, it is divided into proteome, genome, transcriptome, structure analysis, population genetics, and so on. |
Accessed on 4 May 2022. |
Integrated platform of agricultural biological databases and related resources |
It is a consortium of agricultural biological databases that integrate standards and best practices for the acquisition, display, and reuse of genomic, genetic, and breeding data. |
https://phytozome.jgi.doe.gov/pz/portal.html Accessed on 4 May 2022. |
Plant Comparative Genomics Repository |
Phytozome database, the Plant Comparative Genomics portal of the Department of Energy’s Joint Genome Institute, provides a hub for accessing, visualizing, and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets sequenced elsewhere. |
Accessed on 4 May 2022. |
Platform for Crop EST sequences and related molecular information |
HarvEST database includes various functions, such as microarray content design, SNP identification, genotyping platform design, comparative genomics, and the coupling of physical and genetic profiles. |
Accessed on 4 May 2022. |
Protein sequence and functional information resource database and analysis platform |
Uniprot database is the world’s leading resource for high-quality, comprehensive, and freely accessible protein sequence and functional information. |
Accessed on 4 May 2022. |
Plant Genome Sequence Database |
Plantgdb database includes software, visualization, and data access portals that implement novel prediction algorithms, as well as a network infrastructure environment implementation of development tools for distributed computing, protocol sharing, and analysis of source records. |
https://mpss.danforthcenter.org/index.php Accessed on 4 May 2022. |
NGS database, including small RNAs and genome resources for plants |
Meyers Lab database focuses on many aspects of plant small RNAs, including their major roles in gene and transposable regulation, but also their biogenesis and evolution. Includes small RNA sequencing, cut target RNA sequencing, and a variety of informatics tools. |
http://metacrop.ipk-gatersleben.de Accessed on 4 May 2022. |
Crop Metabolism Pathway Database |
Metacrop database summarizes various information about metabolic pathways in crops and allows the automatic export of information to create detailed metabolic models. |
URL |
Note |
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Accessed on 4 May 2022. |
The most commonly used repository of Arabidopsis genetic and molecular biology data |
Accessed on 4 May 2022. |
Arabidopsis cDNA, mutant, and microarray database |
Accessed on 4 May 2022. |
A genome-wide database of putative transcription factor binding sites in Arabidopsis |
Accessed on 4 May 2022. |
Arabidopsis plastid protein database |
Accessed on 4 May 2022. |
Database of key Arabidopsis developmental genes |
Accessed on 4 May 2022. |
Subcellular localization database for Arabidopsis proteins |
Accessed on 4 May 2022. |
Arabidopsis transcriptional regulatory mapping database |
http://wanglab.sippe.ac.cn/rootatlas/ Accessed on 4 May 2022. |
Arabidopsis root single-cell RNA-seq database |
http://ipf.sustech.edu.cn/pub/athrna/ Accessed on 4 May 2022. |
Arabidopsis RNA-seq data resources |
Accessed on 4 May 2022. |
A database showing all T-DNA insertions and methyl group data |
URL |
Note |
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http://www.ricedata.cn/index.htm Accessed on 4 May 2022. |
National Rice Data Center |
http://signal.salk.edu/cgi-bin/RiceGE Accessed on 4 May 2022. |
Rice functional genome expression database |
https://shigen.nig.ac.jp/rice/oryzabase/ Accessed on 4 May 2022. |
Rice genetics and genomics database |
Accessed on 4 May 2022. |
Wheat genome information database |
http://earth.nig.ac.jp/~dclust/cgi-bin/index.cgi Accessed on 4 May 2022. |
Barley germplasm resources and genome analysis database |
Accessed on 4 May 2022. |
Maize genome database |
Accessed on 4 May 2022. |
Maize genome and genetic analysis platform |
Accessed on 4 May 2022. |
Soybean genomics and molecular biology database |
http://www.ildis.org/LegumeWeb/ Accessed on 4 May 2022. |
International legume database and information service |
Accessed on 4 May 2022. |
Cotton genomics, genetics, and breeding database |
Accessed on 4 May 2022. |
Tomato functional genome database |
http://ted.bti.cornell.edu/epigenome/ Accessed on 4 May 2022. |
Tomato epigenome database |
Accessed on 4 May 2022. |
High-resolution mapping and search tool for tomato genes and their products |
http://tomexpress.toulouse.inra.fr/ Accessed on 4 May 2022. |
Tomato transcriptome data visualization and analysis platform |
Accessed on 4 May 2022. |
Genome sequencing database of Solanaceae species |
http://gabipd.org/projects/Pomamo/ Accessed on 4 May 2022. |
Potato bioinformatics database |
Database Name |
URL |
Note |
---|---|---|
Tbtools |
https://github.com/srbehera11/stag-cns Accessed on 4 May 2022. |
An integrated toolkit for interactive analysis of big biological data |
SMART |
http://smart.embl-heidelberg.de/ Accessed on 4 May 2022. |
Protein conserved domain prediction tool |
STAG-CNS |
https://github.com/srbehera11/stag-cns Accessed on 4 May 2022. |
A sequentially conserved non-coding sequence discovery tool for an arbitrary number of species |
FED |
Accessed on 4 May 2022. |
Genome editing exogenous component detection platform |
MAFFT |
https://mafft.cbrc.jp/alignment/server/ Accessed on 4 May 2022. |
Online sequence matching tool |
Protter |
http://wlab.ethz.ch/protter/start/ Accessed on 4 May 2022. |
Online protein structure mapping tool |
EvolView |
https://www.evolgenius.info/evolview/ Accessed on 4 May 2022. |
Web-based tools for visualizing, annotating, and managing system trees |
iTOL |
Accessed on 4 May 2022. |
Online tool for displaying, annotating, and managing system development trees |
Database Name |
URL |
NOTE |
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BAR |
http://www.bar.utoronto.ca/welcome.htm Accessed on 4 May 2022. |
Plant biology analysis tools platform |
CRISPR-P |
http://crispr.hzau.edu.cn/CRISPR2/ Accessed on 4 May 2022. |
Improved CRISPR/Cas9 toolkit for plant genome editing |
ACT |
https://www.michalopoulos.net/act/ Accessed on 4 May 2022. |
Arabidopsis co-expression analysis tool |
OryGenesDB |
Accessed on 4 May 2022. |
An interactive tool for reverse genetics studies in rice |
T-DNA Express |
http://signal.salk.edu/cgi-bin/tdnaexpress Accessed on 4 May 2022. |
Arabidopsis gene targeting tool |
Plant MetGenMAP |
http://bioinfo.bti.cornell.edu/cgi-bin/MetGenMAP/home.cgi Accessed on 4 May 2022. |
Web-based tools for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways |
iTAK |
http://itak.feilab.net/cgi-bin/itak/index.cgi Accessed on 4 May 2022. |
Software packages for identifying and classifying plant transcription factors and protein kinases |
PlantPAN |
http://plantpan2.itps.ncku.edu.tw/ Accessed on 4 May 2022. |
Tools for detecting transcription factor binding sites in plants |
SnpHub |
http://guoweilong.github.io/SnpHub/ Accessed on 4 May 2022. |
A unified web server framework for exploring large-scale genomic variation data |