Tools and Databases
* for recommended
Tools
GO analysis
KEGG analysis
Promoter analysis
Subcellular localization Prediction
- PSI-predictor
- WoLF PSORT or WoLF PSORT
- iPSORT
- cNLS Mapper - Nuclear localization signals (NLSs)
- SignalP 5.0 - Signal peptide and cleavage sites
- ChloroP-1.1 - Chloroplast transit peptides and cleavage sites
- TargetP 2.0 - Mitochondrial, chloroplastic, secretory pathway
Plot
- GSDS2.0 - Gene structure
- Diagrams - Flow chart
- Baidu Naotu - Flow chart
- MapChart - Map chart
- Evenn - Venn Diagrams
- ImageGP - Online plot
Databases
Genome
- PLAZA*
- Phytozome*
- ONEKP*
- Ensembl Plants
- CoGe
- GDA - Genome Database for Angiosperms
- Fernbase
- Published Plant Genomes
- GreenPhylDB v5
- PGSB - Plant Genome and Systems Biology
- MaizeGDB - for maize
- MarpolBase - Genome Database for Marchantia polymorpha
- Marchantia - for Marchantia
- CuGenDB - Cucurbit Genomics Database
- CucCAP – Harnessing genomic resources in cucurbit crops
- Sol Genomics Network - for Solanaceae
Expression
- BAR*
- CoNekT*
- CoNekT - diurnal-tools
- Rice Expression Profile Database (RiceXPro) - for rice
- Rice Expression Database (RED) - for rice
- OryzaExpress - for rice
Gene function
- The Arabidopsis Information Resource (TAIR)
- The Rice Annotation Project (RAP)
- Rice Genome Annotation Project
- Oryzabase - for rice
- funRiceGenes - for rice
Nature variation - Rice
- RiceVarMap v2.0
- GWAS Atlas
- ECOGEMS
- IC4R - Rice Variation Database
- Rice SNP-seek database
- MBKbase
- RFGB - Rice Funcational Genomics & Breeding
Transcription Factor (TF)
- PlantRegMap* - Plant Transcriptional Regulatory Map
- TAPscan - Transcription associated proteins (TAPs)
- GRASSIUS - Grass Regulatory Information Server
Interaction Networks
Small RNA
- miRBase - the microRNA database
- miRTarBase - The experimentally validated microRNA-target interactions database
- PmiREN - Plant miRNA ENcyclopedia - A comprehensive functional plant miRNA database
- miRNEST 2.0 - an integrative approach in microRNA search and annotation
- PsRobot - a web-based plant small RNA meta-analysis toolbox
- psRNATarget - A Plant Small RNA Target Analysis Server (2017 Update)
- sRNAanno - a database repository of uniformly annotated small RNAs in plants
scRNA-seq
- Single Cell Expression Atlas*
- PlantscRNAdb* - A Database for Plant Single-cell RNA Analysis
- Arabidopsis Shoot Cell Atlas
- Arabidopsis Root Cell Atlas
- The Arabidopsis Root scRNA-Seq Atlas