Tip: Using Export to create new tracks
When exporting the track data, a user is presented with a data grid that can be customized. We can use this to create an output file in CSV format that can be imported back to create a new track. For...
Blog
Another major feature upgrade: Export track data
We have made a significant step forward by adding a few new features. One of them is a powerful module for exporting data from the Persephone database. This can be done in an interactive way by using a graphical user...
Major version upgrade: variants
We are happy to introduce a major new feature in the web version: a specialized interface designed to analyze genotyping samples with SNPs and indels. The variant data for thousands of individuals are displayed as a new type of track...
A pair of beet (Beta vulgaris) genomes have been added
The newly published Beta vulgaris EL10_1.0 genome has been uploaded to our web portal to accompany another beet genome RefBeet-1.2.2. The two assemblies can be aligned by connecting gene ortholog pairs (bookmark) Please let us know if loading other tracks for...
BAM tracks can be loaded permanently
The Persephone genome viewer normally visualizes the data stored in a database. The users can add their own tracks (visible to them only) by loading external files. Among the supported types of user tracks are the tracks with NGS read...
Three coffee genomes added
Our collection of genomes at the web portal has three new additions: Coffea arabica, Coffea eugenioides, and Coffea humblotiana. All three genomes can be aligned to each other using the gene ortholog pairs. As usual, this reveals the synteny and...
Rice genome IRGSP-1.0 has now 5 annotation tracks
With our colleagues from KAUST and other organizations, we are preparing the new publication on the analysis of 18 reference genomes from the "Rice Platinum Standard". The pre-print has been submitted to bioRxiv (Pan-genome inversion index reveals evolutionary insights into...
New human genome version CHM13v2 uploaded
We added the Homo sapiens genome version CHM13 from Telomere-to-telomere consortium (https://sites.google.com/ucsc.edu/t2tworkinggroup/). The new data set provides additional sequences missing from the GRCh38 genome project. The authors claim that their technology allowed the addition of 200 Mbp of new sequences. The...
Another scientific paper references Persephone
A study on predicting promoters of several conifer species has been published by International Journal of Molecular Sciences (link). The paper called Genome-Wide Prediction of Transcription Start Sites in Conifers references Persephone's web portal used as the repository of the...
A new feature in the desktop version: Export connector clusters as ribbons
The synteny matrix in the desktop version of Persephone that visualizes the alignment of entire genomes has a useful feature - clustering the connectors in the dot plot. Collinear connectors between orthologs or markers appear as a series of dots...