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...
We have compiled a table that lists the features of the two versions of Persephone. This will help overview the milestones for the development roadmap. In general, we plan to port the most of the features of the Windows version...
The Desktop (Windows) version can now show a new type of track: the sequence conservation track (indicated by the red arrow in the pictures below). The visual elements in this type of track designate the regions linked by the ribbon-like...
In collaboration with our colleagues from KAUST, we have added 21 reference-quality rice genome assemblies to our web portal and to the demo Windows version. Os GJ-temp: IRGSP-1.0 (Nipponbare)Os GJ-subtrp: CHAO MEOOs GJ-trop1: AzucenaOs GJ-trop2: KETAN NANGKAOs cB: ARC 10497Os...
The map set property form in the Windows version of Persephone has now a new tab: Statistics. It lists a few metrics of the genomic sequences of the map set, such as the total sequence length, the percentage of the...
We have added the data for 26 Zea mays reference genomes from the pan-genome project "Whole-Genome Assembly of the maize NAM founders" (https://nam-genomes.org/). The source files were downloaded from MaizeGDB.org. To help browsing this pan-genome data set and provide the...
This week's addition is a pair of citrus genomes: C.sinensis (sweet orange) and (pomelo). We uploaded the genomic sequences with annotation tracks to the Desktop and Web versions. As usual, a routine alignment of syntenic chromosomes reveals large structural rearrangements. We...
The update has a few technical improvements that make loading the marker data much faster. This is done by storing and transmitting the markers in specially-compressed binary blobs. The Synteny matrix has now an improved responsiveness, partially due to more efficient...
In addition to an older Wm82.a2.v1, we have now the version Wm82.a4.v1 of the soybean genome. We added the new data set to the Desktop and to the Web versions. Connecting similar genes helps visualizing the changes between the two...
The genome sequences and gene annotation of Solanum lycopersicum (tomato SL3.0) have been loaded from Phytozome v.13. We added NCBI's Gnomon gene models too, for comparison. Sequences of a close relative, potato, can be aligned to the tomato chromosomes by linking the...