SAM flags are part of the Sequence Alignment Map (SAM) file format. These flags are bitwise values that describe various properties of a read in a SAM file, such as whether it is paired, mapped, reversed, or a duplicate. The...
Persephone uses tables in multiple parts of the interface. We have added extra context menus to most of them, providing control over the way the data is displayed. For example, users can now edit columns by selecting checkboxes in the...
At a certain level of zoom, when it is possible to distinguish individual bases, we provide an option to display the translation of the genomic sequence in 3 frames. Showing the opposite strand can also add three more translation frames....
We significantly increased the limits on the amount of data displayed in BAM/CRAM tracks. There can be genomic regions with a large number of mapped reads. Persephone can now handle peaks of up to 300,000 reads. Naturally, they all will...
To enhance the visibility of protein-coding segments (CDS) in gene model glyphs, we are now displaying introns within the CDS differently from those in the untranslated regions. This improvement will aid in visualizing human genes that are known for their...
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...