Blog

Potato DM_v4.03 and tomato SL3.0 genomes have been added

22:25 21 February in Web Version
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We have loaded the potato genome (DM_v4.03) with multiple annotation tracks showing gene models, mapped markers and repeats. To help assessing the gene prediction quality, we downloaded 300,000 potato EST and mRNA sequences from NCBI and splice-aligned them to the genome. This produced a track with transcripts showing exact location of active splice sites. Most of the predicted genes are consistent with the alignments, though some of them have serious problems (see the locus on the left): Another Solanum species, tomato (version SL3.0), has also been added to the database. Connecting the orthologous tomato and potato genes shows a good synteny between...

Persephone at PAG XXVII – 2019

11:34 27 January in General News
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This was our second year attending the largest Ag-Genomics meeting in the world in San Diego CA. Many thanks to all who stopped by our exhibit as well as those who attended Max Troukhan's talk at the IWGSC workshop (https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/36359) where he demonstrated the wheat genome data visualized in Persephone. We had a steady stream of visitors to our booth all of whom had sincere interest in our product. The interactions that we had will definitely play a role in shaping our product in the future. Some of the highlights of this year’s exhibit were our newly added features and enhancements to...

Mars Wrigley Confectionery licenses Persephone

18:39 12 November in General News
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We are pleased to welcome Mars Wrigley Confectionery into the growing community of Persephone users. We are looking forward to a fruitful collaboration that will make the work of Mars’ scientists more comfortable and productive, while allowing the Persephone team to benefit from their experience in order to further improve the software....

Web version: Users can edit the map set tree

17:04 12 September in Web Version
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We thought, the users might want to rearrange the map set tree on the left by adding, removing or relocating the nodes. For example, as long as the current demo instance has a random set of genomes loaded, plant biologists may want to remove the node with Homo sapiens maps or leave just one favorite genome, to clear the view: ...

Wheat RH Genetic Maps Have Been Loaded

12:14 24 July in Web Version
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We uploaded  wheat RH Maps (from IWGSC) with marker positions in cM. Persephone automatically links maps by common markers, so if you align a chromosome map based on sequence with a corresponding genetic map, the tracks with markers on both maps will appear to be connected. The same visualization, based on orthologous gene pairs, is also available for showing synteny between chromosomes of wheat and rice. In wheat, if you align A chromosomes vs. B chromosomes, you can visualize similarity and structural rearrangements between them. [caption id="attachment_14943" align="aligncenter" width="399"] Two pairs of sequence-based maps are aligned, showing synteny between chromosomes: A1 vs...

Wheat Genome Data from IWGSC Have Been Released

15:07 09 July in Web Version
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According to wheatgenome.org, all data related to the reference sequence of bread wheat, IWGSC RefSeq v1.0, are available without restriction. We would like to use this opportunity to demonstrate the abilities of the web version of Persephone, a tool specifically designed to deal with large data sets, such as the wheat genome. We just have uploaded the reference sequences assembled into 22 pseudo-chromosomes (14 Gbp) and one annotation track with gene models. The search index and BLAST database are being updated. We plan to populate the database with new tracks on a daily basis, please check it out....