With help from Dr. Zhangjun Fei (Cornell University, cucumberdb.com), we uploaded the dataset containing 37 annotated cucumber (Cucumis sativus) assemblies described in the paper Graph-based pangenome reveals structural variation dynamics during cucumber breeding | Nature Genetics. All 37 genomes have been...
We have added two barley (Hordeum vulgare) genomes: morexV3 and 10TJ18_BPGv2. Both assemblies are available with gene annotation. The ortholog pairs link syntenic maps with wheat and oat chromosomes: Chromosomes from four genomes are aligned: morexV3, 10TJ18_BPGv2, wheat, and oat. The full...
We have added two large genomes for Allium cepa (onion) and Allium sativum (garlic). Both assemblies contain exceptionally long chromosomes, some exceeding 2 Gbp in length. We also located a genetic map for onion on Figshare that includes marker coordinates anchored...
We had a great time at the Plant and Animal Genome Conference in San Diego. Our exhibit booth and workshop drew strong interest, and it was a pleasant surprise to see several speakers highlight Persephone in their scientific presentations, which...
The Persephone version, published recently, presents a few improvements. Handling BCF Files In addition to VCF, Persephone now directly supports BCF files imported into the main application. Users can add variants by referencing remote BCF files (with an index) or by loading...
Synteny regions between maps are revealed by linking orthologous genes or common markers. Now you can export these pairs by clicking the button Export visible data in Synteny matrix form. Select two genomes, optionally zoom in on a region of...
If you design an assay targeting a specific allele, it is important to know the genomic sequence neighborhood. A new addition to the Local variants interface will allow users to export flanking sequences around the selected variant. The extracted sequence...
The data for variants loaded from a VCF file can contain sequencing coverage depth (the DP tag in the INFO field). We now allow the automated creation of a quantitative track that stores these DP values. This feature will work...
VCF files used for loading variation data can contain symbolic allele notations, such as <DEL>, <INS>, or <DUP>. These symbolic alleles appear in the ALT field of a VCF record and are used when the actual inserted or deleted sequence...
We have improved the motif search interface, enabling users to search for multiple motifs by entering them as a comma-separated list. Additionally, users can now select DNA motifs from the REBASE database, which contains recognition sites for restriction enzymes. To...