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...
You might like the latest enhancements of the Persephone UI. The users have been able to adjust track feature colors and change the font size. In the new version, we introduced the Dark Mode. Using bright colors against a dark background...
We have added a helpful enhancement to the BLASTN results form: the subject sequences for each HSP can be included in the multiple alignment interface. For instance, you can select a region of interest and use its sequence as a...
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...