Database Resources

WheatOmics requires that all data generated in a study described in a manuscript considered for publication is made available to the broader community in publicly held databases when available, and at the WheatOmics web site, when they are not. The following list of public databases and resources serves as an introductory guide to data analysis and submission for authors contributing to WheatOmics. However, this list should not be considered to be comprehensive. Authors who are aware of additional databases or resources beneficial to other contributors, which are not mentioned here, are encouraged to reach out to WheatOmics with this information.

1 National Center for Biotechnology Information (NCBI)

Provides access to genomic information in order to advance science.

2 GrainGenes

GrainGene a database for Triticeae and Avena, is a comprehensive resource for molecular and phenotypic information for wheat, barley, rye, and other related species, including oat.

3 International Wheat Genome Sequencing Consortium (IWGSC)

The International Wheat Genome Sequencing Consortium

4 WheatOmics

A platform combining multiple omics data to accelerate functional genomics studies in wheat.

5 Ensembl Plants

Hosts the RefSeq v1.0 assembly from the IWGSC,

6 Wheat@URGI

The portal maintains databases and tools to study genetic and genomic wheat data.

7 T3/wheat

T3 is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP).

8 BarleyGenes - Barley RNA-seq Database

This website provides access to the predicted genes from an assembly of whole-genome-shotgun sequence from barley (cv. Morex).

9 Wheat SnpHub Portal

Genomic variation datasets of wheat and its progenitors.

10 Triticeae-GeneTribe

Collinearity-incorporating homology database for Triticeae genomes.

11 Chinese Spring Chromatin State Database

A chromatin state interface for Chinese Spring bread wheat

12 Wheatis Earlham Blast

Bian. X, Tyrrell. S, Davey R.P. The Grassroots life science data infrastructure (2017).

13 AutoCloner

AutoCloner is a custom pipeline that designs homeologue-specific primers for polyploids. It achieves this by extracting SNP locations unique to your gene of interest, and placing the 3` ends of primers at these SNPs

14 PaperBLAST

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, and the Fitness Browser. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

15 CRISPR-Cereal

CRISPR-Cereal: A Guide RNA Design Tool Integrating Regulome and Genomic Variation for Wheat, Maize and Rice.

16 Wheat Panache

a pangenome graph database representing presence/absence variation across 16 bread wheat genomes.

17 WheatComp Database

Genetic Relationship Information Database for Wheat Germplasms

18 Triti-Map

Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

19 KEGG

Database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

20 Gene Ontology Resource

To develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life.

21 GenBank

Genetic sequence database, is an annotated collection of all publicly available DNA sequences.