Informatic Tools

Analysis
Download / Query
Legacy tools
Search
Sequence search
Visualize / Browse

Analysis

GO Enrichment Analysis
GO term enrichment analysis tool
Northern Uniform Soybean Trials (NUST)
Phenotypic reports for the Northern Uniform Soybean Trials (NUST) from 1989 to present

Download / Query

Datastore
Browser interface to all of the files in SoyBase.
GlycineMine
GlycineMine: an InterMine interface for most of the data at SoyBase, including genetic data. Tools include a powerful query engine.
Data Overviews for soy genomic data
Overviews of data characteristics at SoyBase and LIS: genome assembly sizes, gene counts, BUSCO coverage, etc.
USDA Germplasm SoySNP50K
USDA Germplasm collection SoySNP50K Haplotypes: downloads, viewing on browsers, etc.

Legacy tools

GRIN Data Explorer
Legacy SoyBase tool: Search for the GRIN descriptor data
Gene Expression Explorer
Legacy SoyBase tool: Gene expression resources for soybean

Search

Gene-name translator
Find corresponding gene IDs between accessions
Gene Search Tool
Search for genes
Trait Search Tool
Search for trait associations
SoyCyc
Search for genes, proteins, metabolites or pathways

Sequence search

SoyBase SequenceServer BLAST
Run BLASTs against LIS genomes, CDSes, and proteins
Annotate Your Sequences
Functionally annotate protein or nucleotide sequences and place them into gene trees

Visualize / Browse

Genome browsers
Genome browsers for soybean and related species. (Also accessible from the GENOMICS tab)
Genome Context Viewer for Glycine
Browser for dynamically discovering and viewing genomic synteny across selected species.
ZZBrowse GWAS/QTL
Interactive visualization of multiple GWAS and QTL data sets, using synteny to identify potentially conserved association regions between species.
CMap-js: Genetic Map Viewer
View genetic and comparative maps.
LIS Germplasm GIS Viewer
View GIS location information for soybean accessions.
Expression Resources
Gene expression resources for soybean.
GCViT: SNP Comparison Tool
A multiple chromosome visualisation tool for visualizing resequencing or SNP array data
Ontology
SoyBase Soybean growth, development and structural ontology.
Parentage
Soybean parentage and pedigrees