Table 3 Important Databases and Repositories of Genomic Information

Genbank

General public sequence repository

http://www.ncbi.nlm.nih.gov/genbank/

EMBL

General public sequence repository

http://www.ebi.ac.uk/embl/

DDBJ

General public sequence repository

http://www.ddbj.nig.ac.jp

NCBI

Biomedical and genomic information

http://www.ncbi.nlm.nih.gov/

GOLD

Repository of genome databases

http://genomesonline.org/cgi-bin/GOLD/bin/gold.cgi

Phytozome

Genomic plant database

http://www.phytozome.net/

Plantgdb

Genomic plant database

http://www.plantgdb.org

CropNet

Genomic plant database

http://ukcrop.net/

CPGR

Phytopathogen genomic resource

http://cpgr.plantbiology.msu.edu/

Gramene

Cereals information resource

http://www.gramene.org/

R-PAN

Rice pan-genome browser for ~ 3000 rice genomes

http://cgm.sjtu.edu.cn/3kricedb/

Rice SNP-seek

A new SNP-calling pipeline

http://snp-seek.irri.org/

CerealsDB

Genotyping information for over 6000 wheat accessions

https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php

SoyBase

Soybean information resource

http://soybase.org/

MaizeGDB

Maize information resource

http://www.maizegdb.org/

Tair

Arabidopsis information resource

http://www.arabidopsis.org/

SGN

Solanaceae information resource

http://solgenomics.net/

Gene Index Project

Transcriptome repository

http://compbio.dfci.harvard.edu/tgi/

UniProt

Protein sequences and functional information

http://www.uniprot.org/

Swiss-Prot

Protein Sequence database

https://www.expasy.org/resources/uniprotkb-swiss-prot

Protein Data Bank (PDB)

Repository for the 3D structural data of proteins and other biological macromolecules

https://www.rcsb.org/

Gene Ontology (GO)

Describe gene and protein functions across species and databases

https://geneontology.org/

InterPro

Integrates predictive models (known as signatures) from multiple databases into a single resource for protein classification

https://www.ebi.ac.uk/interpro/

KEGG

Annotations for genes and proteins, including their roles in pathways

https://www.genome.jp/kegg/

Pfam

Information on protein families and domains

http://pfam.xfam.org/

STRING

Database of known and predicted protein–protein interactions

https://string-db.org/

BioGRID

Database of protein and genetic interactions, chemical interactions, and post-translational modifications

https://thebiogrid.org/

PhosphoSitePlus

Comprehensive resource for the study of protein post-translational modifications

https://www.phosphosite.org/homeAction.action