Allows users to query, visualize, analyze, and compare plant genome and pathway data across crops and model species. Gramene is a resource that uses information generated from projects supported by public funds to improve the study of cross-species comparisons. The database provides a search interface, and views and functionalities for Plant Reactome. It also shares infrastructure, specialized software components and pre-computed data with Ensembl Plants.
A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
A database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1,479 rice accessions. It is free and open to the public with comprehensive functions.
Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome, genetic map, SNP collections and high throughput genotyping platforms applied to the competitive development of new cultivars, with improve fruit quality and disease resistance. All these tools are being essential to assist a competitive breeding process in the species obtaining varieties with resistance to pests and diseases and with improved fruit quality.
A multi-species database to disentangle the SNP chip jungle. Features of SNPchiMp include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines.
A sorghum genome SNP database. SorGSD covers a diverse collection of 48 sorghum lines that fall into four groups, viz., improved varieties, landraces, wild and weedy sorghums, and a wild relative Sorghum propinquum. SorGSD provides a detailed summary of SNP information and their relevant annotations for all individual accessions, such as allele information, gene information, SNP density and external links to other resources.
Provides genome sequence/variant information for wild Oryza species together with that of several cultivated strains, in close collaboration with Oryzabase, ensuring easy access to information about geographical origins, phenotypic traits, mutants and genetic resources. The current version of OryzaGenome consists of genomic variants from 446 O. rufipogon accessions derived by an imputation method and variants from 17 accessions by imputation-free deeper (up to approximately 90×) sequencing along with the Os-Nipponbare-Reference-IRGSP-1.0 reference genome of O. sativa ssp. japonica cv. Nipponbare. Our goal is to establish a pan-Oryza genomic repository that covers both reference genome sequences and genomic variant information.