The Cannabis pangenome from the Michael Lab at the Salk Institute is now available in Persephone. With previously loaded genomes from NCBI and CSGDB, our collection has 97 assemblies with gene annotation. We also calculated orthologous gene pairs, which allow...
The Persephone version, published recently, presents a few improvements. Drag-and-drop VCF files. Users are now able to import their VCF files. The remote files are referenced by a URL, and the local files can be added via drag-and-drop. For files larger than...
Genetic variations impact gene translation beyond simple amino acid substitutions. A single nucleotide change or indel can disrupt a splice site, altering the final polypeptide product of a gene. Our "Translation Changes" interface highlights variants that lead to modified protein...
When you select genotyping samples, they are shown in the Variants track. Zoom deep enough to see the individual bases and click on one of the variants. The Local variants dialog will open. Local variants form. The formatted table can now...
For version 10.3.9284 and later Until recently, the only way to visualize and analyze variants was to load VCF files into the database using our loader tool, PersephoneShell. This CPU-intensive process transformed the data, making it suitable for fast retrieval in...
As you probably know, Persephone allows users to upload their files and view them alongside the data from the database. When importing annotation files in GFF3 format, the users must select the genome on which they want to see the...
The new tool aligns multiple protein sequences. You can access the alignment interface via the Tools menu. In this case, the text box for the sequences will be empty, and you can populate it with the sequences you wish to...
Our data-loading tool, PersephoneShell, has a new command to run minimap2 for two genomes and create synteny ribbons that connect regions with high sequence similarity. Launching the synteny analysis is very easy; just provide two identifiers (MapSetId) of the genomes to...
We’ve introduced a new video tutorial showcasing the multi-map mode, designed to provide a compact and intuitive view of multiple syntenic maps. To get started, simply open a blank screen via Tools → Multimap and select a main reference map. The...
It might look simple - to change straight connecting lines to curvy splines - but using standard graphics libraries to draw thousands of Bezier curves will not provide adequate rendering speeds. We had to delve deeply into the GPU shader...