Please welcome new members of our genome collection: Mouse mm39 (Mus musculus, GRCm39) and Gorilla Kamilah_GGO_v0 (Gorilla gorilla). As usual, we identified orthologous gene pairs between these genomes and the human genomes. This has allowed us to produce synteny matrices...
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...
Please check out the new genome added to Persephone. It has been downloaded from NCBI's RefSeq with the latest gene annotation generated just a week ago. A celery chromosome is aligned with a carrot chromosome based on orthologous gene links The...
The new version Wm82.a6.v1 of the soybean genome has been loaded to Persephone. The sequence has sometimes-substantial differences from the previous version (Wm82.a4.v1). The analysis of the new assembly by Mary Jane C. Espina et.al. has been published here. Our collection...
We're excited to share that CoverCress Inc. has licensed Persephone, our advanced genome visualization platform! This collaboration marks a significant step forward in the development of the CoverCress crop (domesticated pennycress). CoverCress Inc. (CCI) is leading the way in transforming pennycress into a sustainable, high-value oilseed using...
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...