Informatic Tools

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

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.

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

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