We just came back from the Plant and Animal Genome conference in San Diego. For three days of the exhibits, we were meeting scientists who expressed interest in Persephone at our booth. We are always happy to listen to the users'...
We added genomes from the Drosophila genus: D.melanogaster, D.simulans, and D.yakuba. For now, the sequences are annotated using RefSeq gene models from NCBI. Aligning and comparing the genomic sequences by the ortholog genes reveals clear structural rearrangements. Synteny matrix comparing two full...
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...
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...
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...
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...
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...
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...
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...
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...