Databases URL Description
TAIR www.arabidopsis.org The Arabidopsis Information Resource (TAIR).
sRNAanno www.plantsrnas.org Plant Small RNA Annotation Database.
PlantRegMap http://plantregmap.gao-lab.org/binding_site_prediction.php Plant Transcriptional Regulatory Map.
Phytozome https://phytozome-next.jgi.doe.gov/ Phytozome, the Plant Comparative Genomics portal, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes.
MaizeGDB https://maizegdb.org/ MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.
CPBD http://citrus.hzau.edu.cn/ Citrus Pan-genome to Breeding Database.
SGN https://solgenomics.net/ The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.
miRbase https://www.mirbase.org/ miRBase is the primary public repository and online resource for microRNA sequences and annotation.
GDR https://www.rosaceae.org/ GDR: the Genome Database for Rosaceae.
WheatOmics http://wheatomics.sdau.edu.cn/ WheatOmics: a platform combining multiple omics data to accelerate functional genomics studies in wheat.
WheatComp Database http://wheat.cau.edu.cn/WheatCompDB/ Genetic Relationship Information Database for Wheat Germplasms.
Rice Genome Annotation Project http://rice.uga.edu/ The Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome.
Rice Genome Annotation Project http://rice.uga.edu/ The Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome.
Database Commons https://ngdc.cncb.ac.cn/databasecommons/ Database Commons: a curated catalogue of worldwide biological databases.
Database Commons https://ngdc.cncb.ac.cn/databasecommons/ Database Commons: a curated catalogue of worldwide biological databases.
PlantGDB http://www.plantgdb.org/ Tools and resources for plant genomics.
PlantCARE http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ PlantCARE, a plant cis-acting regulatory element database.
PlantTFDB http://planttfdb.gao-lab.org/ Plant Transcription Factor Database.
1001 Genomes https://1001genomes.org/ A Catalog of Arabidopsis thaliana Genetic Variation.
Arabidopsis RNA-seq Database http://ipf.sustech.edu.cn/pub/athrna/ A Comprehensive Online Database for Exploring ∼20,000 Public Arabidopsis RNA-Seq Libraries.



Tools URL Description
TBtools https://github.com/CJ-Chen/TBtools/releases a Toolkit for Biologists integrating various biological data-handling tools.
sRNAminer https://github.com/kli28/sRNAminer sRNAminer: a Multifunctional Toolkit for Next Generation Sequencing Small RNA Data Mining.
IGV-sRNA http://plantsrnas.org/software.html IGV-sRNA is developed on the basis of IGV, and is specifically optimized for small RNA data visualization.
CRISPR-GE http://skl.scau.edu.cn/ A toolkit for CRISPR-based genome editing.
Mapman4 https://mapman.gabipd.org/ MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.
Smart http://smart.embl-heidelberg.de/ For identification and annotation of protein domains and the analysis of protein domain architectures.
Expasy https://www.expasy.org/ Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics.
Trinity https://github.com/trinityrnaseq/trinityrnaseq/wiki Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
ClusterProfiler https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html A universal enrichment tool for interpreting omics data.
Cytoscape https://cytoscape.org/ Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Kingfisher https://github.com/wwood/kingfisher-download Kingfisher is a fast and flexible program for procurement of sequence files (and their annotations) from public data sources, including the European Nucleotide Archive (ENA), NCBI SRA, Amazon AWS and Google Cloud.
eggNOG http://eggnog-mapper.embl.de/ EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed Orthologous Groups (OGs) and phylogenies from the EggNOG database to transfer functional information from fine-grained orthologs only.
KofamKOALA https://www.genome.jp/tools/kofamkoala/ KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold.