SoyBase Follow us on Twitter @SoyBaseDatabase
Integrating Genetics and Genomics to Advance Soybean Research

Pan-Genome Sequence Search and Data Download Page

In this form you can BLAST your sequences to individual cultivar transcript or gene sequences in the SoyBase Soybean Cultivar Genomes Collection or perform a Pan-genome analysis by comparing your input sequence to all the protein or nucleic acid sequences of all of those contained in the SoyBase Soybean Cultivar Genomes Collection. You can also download individual cultivar's genomic or gene model sequences

Select a genome to query. Pick "All Listed G.max Genomes" or "All Listed G.soja Genomes" to perform a search of all the listed genomes.

Genome Selector
Glycine max Genomes
Cultivar Lee Wm82.a2.v1
Zhonghuang 13 All Listed G.max Genomes

Glycine soja Genomes
Cultivar PI 483463 Cultivar W05
All Listed G.soja Genomes

Select the type of sequence to search. The options are the gene model coding sequences (nucleic acid) or the protein sequence (amino acid).

Sequence Type Gene model transcripts Gene model protein Sequences

Pick the type of BLAST program to run.

Select the BLAST Program to run

Copy-n-paste a gene sequence you want to compare to a cultivar or the pan-genome. You can also choose a file containing multiple FASTA records with which to search.


Or load an Example Sequence.

Clear Sequence
Click Here For The Full BLAST Interface

From this form you can download soybean cultivar genomic, gene model and protein sequences from the SoyBase soybean cultivar genomes collection. The results will be made into a file and transfered to your computer to save.

Choose a genome from which to download sequences.

Glycine max Genomes
Cultivar Lee Cultivar Zhonghuang 13
Cultivar Wm82 Assembly 2

Glycine soja Genomes
Cultivar PI 483463 Cultivar W05

Select the type of sequence to download. The options are the entire genomic sequence (nucleic acid), the gene model transcript sequences (nucleic acid), coding sequences (nucleic acid) or the inferred protein sequence (amino acid) of each transcript.

Sequence Type
Genomic Sequence
Gene model Transcripts
Gene model coding sequences
Gene model Inferred Protein Sequence

Bayer et al. sequenced 1000 accessions from the USDA Soybean Germplasm Collection and assembled the genomes using the cultivar Lee. The collection included wild and cultivated strains to assess genome-wide gene changes due to domestication.

SoyBase Genome Viewer representation of Lee gene presence/absence in 1000 accessions

Files associated with this project

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA
Iowa State University Logo