The latest addition to Persephone’s toolset is an interactive interface for editing gene models. When you encounter an issue in an existing gene model, you can now create your own corrected version of the gene structure and save it so...
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...
Updated: added batch processing 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 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...