We are pleased to announce that The Kazusa DNA Research Institute has licensed Persephone. Our tool will be used at the Institute to provide services such as genome analysis of cultivated plants and related microorganisms, and development of practical technology...
A new work called "Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata" has been published in Nature. The data for the genome of Aegilops umbellulata is hosted at the Persephone web portal. Two of our colleagues (Maxim Troukhan and Maksym...
Minimap2 Our next major feature upgrade of Persephone includes interesting new functions. First of all, we integrated minimap2 - a popular alignment tool that, besides aligning short reads, can be used for sequence comparisons on the scale of full chromosomes. As you...
Our community is growing! Cornell University's School of Integrative Plant Science licensed Persephone. Our new customer uses genomic tools to better understand hybrid vigor, sex determination and pest and disease resistance in shrub willow bioenergy crops. More recently, they have initiated...
The Persephone software stack includes the database, mono (to run .NET binaries on linux), the main server WebCerberus, the loader PersephoneShell and Apache Solr text search engine. Each component can be installed and tuned separately, which in detail is described...
We have added three genomes of Echinochloa grasses. These are weeds known by the common names barnyard grass or corn panic grass. In particular, the species are: Echinochloa oryzicola (late barnyard grass), Echinochloa crusgalli (cockspur (or cockspur grass), barnyard millet, Japanese millet, water grass, common barnyard grass) and Echinochloa...
We have expanded our collection by adding four Brassica genomes: Brassica rapa Fpc_v1.3, Brassica rapa Chiifu v3.5, Brassica oleracea v1.0, and Brassica napus Da-Ae. As usual, aligning chromosomes from different species using Persephone illustrates the structural rearrangements between the organisms....
The web version of Persephone has now a few new features. Highlights Drag the mouse while holding Ctrl key to highlight a region on a map. The highlight is temporary, another selection will remove the previous highlight unless it is made permanent....
Our system at https://web.persephonesoft.com has a couple of newly added cocoa genomes:Theobroma cacao (Criollo v2)Theobroma cacao (Matina v2) Comparing the cocoa genomes to the ones for coffee by using orthologous gene pairs reveals significant synteny. Synteny between chromosome 4 of cacao and...
We added a new functionality to Persephone - it can now accept modbam files with base modification values commonly used to indicate methylation. The files can be imported using either PersephoneShell, which uploads them to the database, or to a...